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

This paper presents a holistic survey of small mammal diversity across the Santa Catalina Mountains conducted from 2021 to 2023, which documented 15 species, extended the known elevational ranges for eight of them, and established a comprehensive model of voucher and non-lethal tissue sampling to address historical data gaps and support future eco-evolutionary research in the Madrean Sky Islands.

The Gist

Imagine the Santa Catalina Mountains in Arizona as a giant, vertical city. At the bottom, near the hot, dry desert floor, you have a bustling marketplace of cacti and lizards. As you climb higher, the air gets cooler and wetter, and the "neighborhoods" change: first to grassy parks, then to shrubby hills, then to open woodlands, and finally, at the very top, to dense, cool pine forests.

For over a century, scientists have been trying to map the tiny residents of this vertical city—the mice, rats, shrews, and squirrels. But until now, their map was full of holes. Most of the data was collected in the 1960s or earlier, like an old, yellowed photograph that doesn't show what's happening today.

The Mission: A Modern "Census" of the Tiny City Dwellers

A team of scientists decided to update this map. They didn't just want to count how many mice were there; they wanted to take a "holistic" snapshot. Think of it like this: instead of just taking a photo of a person, they also took their DNA, checked their health, looked at the bugs living on them, and preserved their story for the future.

They set up a grid of traps (like tiny, safe hotel rooms with oatmeal snacks) across 10 different "neighborhoods" from the desert floor to the mountain peak. Over two years, they caught 369 small mammals.

What They Found: The Plot Thickens

Here are the key takeaways, translated into everyday terms:

1. The "Ghost" Residents: They found a species of mouse (Reithrodontomys fulvescens) that no one had ever officially seen in these mountains before. It's like finding a new neighbor who moved in quietly and no one noticed until now. This suggests that some animals are moving into new areas, perhaps because the climate is changing.
2. The "Moving Up" Trend: Many of the animals they caught were living higher up the mountain than historical records said they should be. Imagine if the squirrels that used to live in the park at the bottom of the hill suddenly started building nests in the pine trees at the top. This "upslope movement" is a classic sign that animals are chasing cooler temperatures as the world gets warmer.
3. The Fire Effect: Two of the places they studied had been burned by a massive wildfire (the Bighorn Fire) just a few years prior. They found that the animals were already moving back in, but the mix of species was changing. It's like a forest that was cleared by a storm; the plants and animals that return are different than the ones that were there before.
4. The "Missing" Neighbors: Interestingly, they didn't find some animals that were known to live there in the past. Some low-desert species seemed to have vanished from the specific spots they checked, possibly due to habitat changes or the heat getting too intense.

Why This Matters: More Than Just Counting Mice

You might ask, "Why do we care about a few mice?"

Think of these small mammals as the canaries in the coal mine for the entire ecosystem.

• The Barometer: If the mice are moving up the mountain, it tells us the plants they eat are moving up, too. If the mice are disappearing, it tells us the habitat is breaking down.
• The Time Capsule: The scientists didn't just catch the animals; they preserved their tissues (frozen like a time capsule), their DNA, and even the tiny parasites living on them. This allows future scientists to study diseases, genetics, and evolution decades from now without having to go back and catch them again.
• The Big Picture: The Santa Catalinas are just one of many "Sky Islands" (mountains surrounded by desert). By understanding how life here is changing, we can predict how other mountains across the Southwest will react to climate change, fires, and drought.

The Bottom Line

Even though the Santa Catalina Mountains are right next to a major city (Tucson) and have been visited by scientists for 140 years, this study proved that we still have a lot to learn. The "vertical city" is changing fast. The residents are moving, the neighborhoods are shifting, and the old maps are outdated.

This paper is a call to action: we need to keep watching, keep measuring, and keep preserving these tiny stories, because they hold the keys to understanding the future of our entire natural world.

Technical Summary

1. Problem Statement

The Madrean Sky Island Archipelago, particularly the Santa Catalina Mountains in Arizona, represents a critical "biogeographic crossroads" where species from the Rocky Mountains and Sierra Madre Occidental converge. Despite being a well-studied region for plants and arthropods, there is a significant knowledge gap regarding terrestrial small mammal diversity.

• Historical Data Deficit: The last comprehensive review of small mammals in the Santa Catalinas was published by Lange in 1960. Approximately 95% of existing voucher specimens were collected prior to 1980.
• Climate Change Context: There is a lack of modern baseline data to assess how small mammal communities are responding to rapid environmental changes, including rising temperatures, prolonged droughts, altered fire regimes (e.g., the 2020 Bighorn Fire), and urbanization.
• Sampling Bias: Historical sampling is heavily biased toward high elevations, low terrain ruggedness, and proximity to roads, leaving mid-elevation and remote areas underrepresented.

2. Methodology

The study employed a holistic, transect-based sampling design from November 2021 to July 2023 to address these gaps.

• Study Area & Design:
  • Surveyed 10 localities across the north and south slopes and the peak of the Santa Catalina Mountains.
  • Sites were selected to represent five major biotic communities: Sonoran Desertscrub, Semidesert Grassland, Interior Chaparral, Madrean Oak Woodland, and Petran Montane Conifer Forest.
  • Two sites (Oak Woodland and Conifer Forest) were located in areas burned by the 2020 Bighorn Fire.
• Sampling Protocol:
  • Effort: 4,000 total trap-nights using 200 Sherman live-traps arranged in transects (3–5 lines per site).
  • Vouchering: Up to 3 individuals per species per site were euthanized (per permit limits) and prepared as vouchers (fluid-preserved, skulls, or study skins).
  • Non-lethal Sampling: Individuals exceeding the lethal limit were sampled for ear clips, feces, ectoparasites, and morphological measurements before release.
  • Holistic Preservation: All vouchers were processed for "extended specimen" preservation, including flash-freezing of multiple tissue types (muscle, liver, kidney, heart, lung, blood smears) for genomic, transcriptomic, and metagenomic analyses.
• Data Integration:
  • Historical Data: Aggregated 1,600 historical records (1916–2020) from GBIF, USNM, and AMNH, filtering for taxonomic accuracy and georeferencing precision.
  • Bias Analysis: Used ArcGIS Pro and R to analyze sampling bias regarding elevation, terrain ruggedness index (TRI), and distance from roads compared to simulated random sampling.
  • Comparative Analysis: Conducted Principal Coordinate Analysis (PCoA) to compare small mammal community composition with previously surveyed plant and arthropod diversity at the same sites.

3. Key Contributions

• Bridging a 40-Year Gap: The study provides the first modern, systematic inventory of small mammals in the Santa Catalinas since the 1980s, effectively bridging a ~40-year lull in specimen preservation.
• Holistic Specimen Preservation: It establishes a new standard for sky island surveys by preserving a suite of frozen tissues alongside traditional vouchers, enabling future studies on host-pathogen interactions, microbiome analysis, and population genomics.
• Baseline for Climate Response: By comparing modern data with a 140-year historical baseline, the study creates a robust "before-and-after" framework to detect elevational shifts and range expansions driven by climate change.

4. Key Results

• Species Diversity:
  • Recorded 15 species of terrestrial small mammals across 9 genera (families: Cricetidae, Heteromyidae, Sciuridae, Soricidae).
  • Collected 150 voucher specimens and 219 non-lethally sampled individuals (totaling 369 identifiable animals).
  • Highest Richness: Semidesert Grassland (9 species), followed by Conifer Forest (7 species).
  • Dominant Species: Peromyscus boylii was the most frequently captured (112 individuals), found in 4 of 5 communities.
• Elevational Range Extensions:
  • The survey extended the known elevational ranges for 8 of the 15 species sampled.
  • Upslope Shifts: 6 species showed upslope extensions (ranging from +11 m to +394 m). Notably, Chaetodipus intermedius and Neotoma albigula extended >100 m upslope.
  • New Detection: The study documented the first known specimen of Reithrodontomys fulvescens in the Santa Catalinas, found in riparian habitat.
  • Range Expansion vs. Extension: While 5 species with sufficient sample sizes ($n \ge 15$) showed statistically supported upslope extensions, the authors caution that distinguishing between statistical sampling artifacts and true biological range expansions requires further spatial occupancy modeling.
• Community Correlations:
  • Small mammal species richness strongly correlated with plant ($r=0.710$) and arthropod ($r=0.790$) richness across the 10 sites.
  • PCoA results confirmed that small mammal community composition is primarily driven by elevation and biotic community type, mirroring patterns seen in plants and arthropods.
• Sampling Bias:
  • Confirmed that both historical and modern sampling are heavily biased toward lower terrain ruggedness and proximity to roads.
  • Historical sampling was concentrated around 2,300 m, while modern sampling successfully filled gaps in mid-elevation and rugged terrain.

5. Significance

• Ecological Insight: The findings support the hypothesis that montane species are shifting upslope in response to climate change, consistent with trends observed in plants and arthropods in the same region.
• Fire Ecology: The detection of species like Neotoma albigula and N. mexicana in a post-fire Oak Woodland suggests that fire-induced habitat changes may alter niche partitioning and species distributions.
• Methodological Model: The paper advocates for a "middle path" in conservation biology: combining limited lethal vouchering (essential for high-quality tissue and skeletal data) with extensive non-lethal sampling. This approach maximizes data utility for future genomic and ecological studies while minimizing impact on sensitive populations.
• Future Research: The study highlights that even accessible, well-studied mountains like the Santa Catalinas harbor undiscovered biodiversity and dynamic range shifts. It calls for similar holistic surveys across the broader Madrean Sky Island Archipelago to create a regional network for monitoring eco-evolutionary responses to global change.