Nate Upham
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n8upham.bsky.social
Nate Upham
@n8upham.bsky.social
780 followers 700 following 95 posts
Evolutionary biologist & Mammalogist at Arizona State University
Rodents of the Sonoran Desert and Sky Islands
Connecting rodent evolution, genomics, & ecology to life's cosmic problems 🌒
\\ Views are my own // #BLM
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n8upham.bsky.social
Impressively, most small mammal specimens (87%) were collected prior to 1980, meaning they were collected without DNA/RNA preservation as a priority.

This work lays the foundation for future fieldwork in the Madrean Sky Islands, especially from undersampled mountains.
September 8, 2025 at 7:46 PM
n8upham.bsky.social
Mexico's 25 sky islands are mostly unsampled (only the San Luis, Sierra dos Ajos, and Sierra La Mariquita have any specimens) and several of Arizona's larger sky islands have fewer than 40 specimens (Galiuros, Canelo Hills, Santa Teresas, Mules, and Dragoons).
September 8, 2025 at 7:46 PM
n8upham.bsky.social
Answer? Mostly on 5 of the 54 sky islands: 79% come from the Chiricahuas, Pinalenos, Huachucas, Animas, and Santa Catalinas.

Only 25 sky islands in the Madrean system have any recorded specimens.
September 8, 2025 at 7:46 PM
n8upham.bsky.social
When & where have species of bats, rodents, & shrews been collected across the 54 mountains of the Madrean Sky Islands?

Damien Rivera in our lab led this effort to find out!

New preprint "Uncovering historical small mammal biodiversity among the Madrean Sky Islands" www.biorxiv.org/content/10.1...
September 8, 2025 at 7:46 PM
n8upham.bsky.social
Sagui centrál! Crew of Black-tufted-ear Marmosets (Callithrix penicillata) at my uncle-in-law's house outside of São Paulo last week 🙏🏻
August 16, 2025 at 11:00 PM
n8upham.bsky.social
Eastern Gray Kangaroos have unique genetics influenced by human-made structures! A study by Urbanek et al. shows that elevation & urbanization can impact their gene flow, highlighting the need to consider both factors in conservation planning #2025MMM #RIP link.springer.com/article/10.1...
New research by Urbanek et al. maps how Eastern grey kangaroos move and mix their genes across the Sunshine Coast. Roads, green spaces, and buildings all shape their pathways, affecting genetic connectivity. Protecting these links is key for their future! [Note: this is a layman's skeet about Fig 6 from Urbanek et al. Actual Fig 6 legend pasted below: Circuitscape-derived weighted current density map illustrating potential M. giganteus gene flow pathways at a fine scale resolution (50 m). A Genetic connectivity mapping of M. giganteus in the Sunshine Coast region, accounting for managed green spaces, major transportation routes, and buildings. B Detailed examination of genetic connectivity among four at-risk populations. Key features include grey lines representing major roadways, green polygons demarcating designated urban green spaces, and purple polygons outlining the extent of existing urban structures. Photo credit: University of the Sunshine Coast]
March 18, 2025 at 2:02 AM
n8upham.bsky.social
A group of Eastern Gray Kangaroos 🦘in Queensland's Sunshine Coast has a unique genetic signature that suggests this area may have been a safe haven for them during ancient climate shifts. 🌏 journals.plos.org/plosone/arti... #2025MMM
"Fig 3. From Coghlan et al (2015): Sampling and haplotype locations. In this genetic map of Eastern grey kangaroos, different shapes show distinct kangaroo family groups across Australia, with a special clade in the Sunshine Coast. Open symbols are past data, while black ones are newly discovered genetic patterns! https://doi.org/10.1371/journal.pone.0128160.g003 [Above text is a layman's explanation in skeet length. ORIGINAL figure text here: Map showing location and haplotype designations of each clade according to the phylogenetic tree. Circles represent the Northern clade, diamonds represent the VIC/TAS/NSW clade, crosses represent the Sunshine Coast clade, squares represent both NSW 1 and NSW 2 clades, and stars represent cities. The open shapes represent haplotypes from Zenger et al. [23] and solid black coloured shapes represent new haplotypes sampled in this paper. Inset is the Sunshine Coast region; shading in inset indicates contemporary temperate rainforest.]"
March 18, 2025 at 1:52 AM
n8upham.bsky.social
Geladas live in multilevel societies w/core units that can form teams/ bands/ communities (small -> large). Snyder-Mackler et al. (2014) used STRs & mtDNA & found that associations among females persisting across generations drives team & band formation. doi.org/10.1111/mec.... #2025MMM
Alt text: Fig. 3 from Snyder-Mackler et al. (2014) (a) Schematic showing a fission event where a large unit (grey circle) fissioned into two or more ‘daughter’ units (white circles). (b) Relatedness within units after fissions (white bar) was significantly higher than relatedness within units prior to fissions (grey bar; P < 0.02, N = 3 fissions, within-unit N = 104 dyads, between-unit N = 108 dyads).
March 18, 2025 at 1:50 AM
n8upham.bsky.social
Fig-eating Bat is gone. Could rapid departure have repercussions? Species richness reaches natural equilibrium. Rapid extinctions - many caused by humans - disrupt it. But scientists can help protect genetic diversity and restore species #RIP #2025MMM www.nature.com/articles/s41...
Estimated times of colonization of each independent colonist lineage, in millions of years (Myr) before present (black horizontal lines show 95% CI). Squares, non-endemic; circles, endemic. Sizes of pie charts are proportional to diversity. Letters next to pie charts correspond to codes in Supplementary Table 2. Illustrations show, from left to right (clade in brackets): Brachyphylla nana (A), Erophylla bombifrons (A), Mormoops blainvillei (B), Desmodus sp. (E), Cubanycteris silvai (H), Phyllops falcatus (I), Pteronotus parnellii (N), Macrotus waterhousii (O). Illustrations by Adrian Tejedor
March 18, 2025 at 1:44 AM
n8upham.bsky.social
The Fig-eating Bat is nocturnal but has a functional OPN1SW color vision gene, unlike many of its close relatives among noctilionoid bats. It's not just gene loss in this lineage—changes in gene expession (usage) play a role as well #2025MMM elifesciences.org/articles/37412
"L and S opsin cone distribution in 14 representative noctilionoid bat species. Density maps of L and S opsin cone topography in 14 noctilionoid bat species. For each species, a representative dissected flat-mounted retina is shown. Insets are representative IHC magnifications "
March 18, 2025 at 1:39 AM
n8upham.bsky.social
Who supports who in Coati social groups? By measuring relatedness using genetic markers, scientists find that coati tend to support close relatives more than unrelated band members. #2025MMM www.sciencedirect.com/science/arti...
"Fingerprint similarity values for the five sampled adult females from KPLT band during 1993 and the proportion of sightings of these individuals as solitary females."
March 18, 2025 at 1:38 AM
n8upham.bsky.social
Just look at the Greater Mouse Deer's lil' tongue there! Practically drooling at the potential for new wild habitat after its reintroduction becomes a reality. But until humans can get out of the way, that drool will mostly be applied to captive breeding. #RIP #2025MMM www.mdpi.com/2071-1050/15...
Study area and occurrence data of greater mouse-deer showing IUCN range. Dark gray areas are the study area, green is calibration points for species distribution modeling
March 18, 2025 at 1:33 AM
n8upham.bsky.social
The Lowland Paca has a one-of-a-kind genetic blueprint that helps confirm where it fits in the rodent family tree! Li et al. (2023) recently sequenced its full mitochondrial DNA, giving us a clearer picture of its evolution. #2025MMM www.tandfonline.com/doi/10.1080/...
Fig 3 from Li et al. (2023). Scientists mapped out the paca’s family tree. By comparing 13 key genes from 26 rodent relatives, they confirmed where the paca fits in the rodent world. The new genetic data (marked in blue) helps fine-tune our understanding of its evolution.
March 18, 2025 at 1:26 AM
n8upham.bsky.social
Greater Mouse Deer on Thai mainland today survive only in captivity. Genetics shows inbreeding/reduced ability to adapt. Are they doomed? Nope! Breeding program = more mouse deer in captivity. Now, urgent habitat improvement needed to support reintroduction #2025MMM www.mdpi.com/2071-1050/15...
Potential habitat suitability modeling of greater mouse-deer in Thailand. (A) Upper Southern of Thailand, (B) Middle Southern of Thailand, and (C) Lower Southern of Thailand.
March 18, 2025 at 1:23 AM
n8upham.bsky.social
Can Bandicoot be saved? Yes, but optimizing source populations is key! When re-establishing populations following local extinction, including individuals from less related populations boosts genetic diversity, supports long-term success #RIP #2025MMM link.springer.com/article/10.1...
Summary of STRUCTURE analyses to group individuals into broad genetic clusters (K) for prioritising sourcing of supplementary individuals. Figure 3A shows mean likelihood values L(K) for different values of K. Figures 3B and C show the spread of cluster membership coefficients among geographic regions and individuals, respectively, with colours representing genetic clusters
March 18, 2025 at 1:20 AM
n8upham.bsky.social
Genetics shows how fragmenting landscapes puts species at risk. Genetic analysis of 15 microsats shows Bandicoots living in 14 forest fragments tend to stay close to home. Strategically placed habitat corridors could help, though! #2025MMM link.springer.com/article/10.1...
Map of the Mount Burr Range in south-eastern South Australia, Australia, in the Green Triangle Forest. Agriculture lands are represented by white shading. Names of the 14 sampled patches appear next to or in the corresponding dark grey areas
March 18, 2025 at 1:10 AM
n8upham.bsky.social
The aardvark's genetic structure is influenced by climate! Research shows that arid regions limit gene flow among aardvark pops, leading to genetic differentiation, suggesting that climate-associated adaptations play a key role in aardvark evolution! onlinelibrary.wiley.com/doi/10.1111/... #2025MMM
Using DNA from fecal samples, a non-invasive technique for genotyping, Epps et al. (2023) identified four genetic clusters separated geographically by arid regions of land. See figure 2. https://onlinelibrary.wiley.com/doi/10.1111/ddi.13792
March 18, 2025 at 1:09 AM
n8upham.bsky.social
Greater glider is a survivor. When forests were replaced w pines in the '60s no one expected them to persist. Decades later, they're still there (but rarer). Remnant native patches hold more genetic diversity than expected, suggesting immigration #RIP #2025MMM onlinelibrary.wiley.com/doi/abs/10.1...
Map of Buccleuch State Forest, New South Wales, showing the extent and position of the Pinus radiata plantation, native eucalyptus forest, cleared farmland, and the sites from which greater gliders, Petauroides volans, were sampled for genetic analyses (shown in black).
March 18, 2025 at 1:03 AM
n8upham.bsky.social
Genetics of Paradise flying snake is mostly a mystery. How much DNA in GenBank? Tiny pieces from just 5 snakes. Brand new paper has first mitochondrial genome for related ornate flying snake. 17,252 bases & 37 genes. It's a start! #2025MMM www.nature.com/articles/s41...
The Phylogenetic tree was constructed through MEGA 7.011 (Kumar et al. 2016) using the Maximum Likelihood method based on the Tamura-Nei model involving 10 complete mitochondrial genome sequences of Colubridae along with their accession numbers.
March 18, 2025 at 12:50 AM
n8upham.bsky.social
Is greater glider just one species ... or three? DNA sequencing of gliders from around Australia suggests 3 "operational taxonomic units" that align with morphology. Defining species is crucial first step in protecting them #2025MMM www.nature.com/articles/s41...
Greater gliders from the northern (top left), central (bottom left) and southern (right) groups identified through DArTseq showing morphological differences that are typical of our dataset. Greater gliders of the type shown on the right have several pelage colour morphs including white and light grey. Photos by Denise McGregor (top left) and Jasmine Vink (bottom left and right).
March 18, 2025 at 12:48 AM
n8upham.bsky.social
Phylogenetic analyses of hedgehogs by Bannikova et al. (2014) show Atelerix albiventris as closest to A. algirus (mtDNA) or maybe A. frontalis (data from 5 nuclear genes) & time estimates suggest these 3 species diverged during the early Pleistocene ~2.3 mya! doi.org/10.1111/bij.... #2025MMM #RIP
Figure 5 from Bannikova et al. (2014): Timescale of major divergence events among taxa of Erinaceidae based on nuclear gene data. The divergence times correspond to the mean posterior estimate of their age in Myr. The bars represent the 95% HPD interval. Numbers above branches correspond to posterior probabilities for each node. Arrows point to nodes for which time constraints were applied.
March 18, 2025 at 12:44 AM
n8upham.bsky.social
Genome sequencing & tissue specific gene expression analyses of hedgehog by Jiang et al. (2024) revealed networks of genes (including a cluster of keratin genes on chromosome 7) acting to create hedgehog’s spines! doi.org/10.1016/j.jg... #2025MMM
From Figure 1 (Jiang et al., 2024) Network comparison between the dorsal and abdominal skin tissues. Nodes are genes indicated by circles (where big circles denote the hubs of networks). Light blue and light brown arrowed lines stand for the activation and inhibition regulation, respectively, with the thickness of lines proportional to the strength of regulation. ASE, allelic-specific expression; TDGs, tandem duplicated genes; EGs, xpanded genes; KRT, keratin; KRTAP, keratin-associated protein.
March 18, 2025 at 12:37 AM
n8upham.bsky.social
Landscape geneticists map patterns of genetic diversity onto geography, and find that for SUN 🌞 BEARS in Cambodia, farms are a barrier to gene flow. Conservation efforts could help promote population connectivity #2025MMM link.springer.com/article/10.1...
Sun bear (Helarctos malayanus) distribution map, altered from the IUCN Red List map (Scotson et al. 2017). The colours represent the confirmed present (green) and probable present (blue) distribution ranges, as well as the areas where the sun bear is assumed to have gone extinct (red).
March 18, 2025 at 12:35 AM
n8upham.bsky.social
Arbogast (2007) analyzed mtDNA Cytb & found that Pacific & Continental NF Squirrel pops are distinct (though nuclear DNA analyses don’t show this) suggesting a complex history associated w/Pleistocene forest contractions & expansions (w/subsequent gene flow) #2025MMM #RIP doi.org/10.1644/06-M...
Neighbor-joining tree showing evolutionary relationships among populations of the 2 species of Glaucomys based on analysis of the mitochondrial DNA cytochrome-b gene (adapted from Arbogast et al. 2005). This tree is presented as a phylogram (branch lengths are proportional except for that between Hylopetes and the ingroup taxa). Bootstrap values. 50% for the outgroup analysis are shown above the line at each node, followed parenthetically by those estimated with the outgroup taxon removed (see Arbogast et al. [2005] for details). Localities (state or province abbreviations and number of individuals showing a given haplotype) are indicated at each terminal branch. Haplotypes found in the endangered southern Appalachian subspecies of G. sabrinus are indicated by asterisks.
March 18, 2025 at 12:31 AM
n8upham.bsky.social
Should Sunda colugo be divided up into multiple species? Janečka et al. (2008) analyzed mitochondrial & nuclear DNA finding unexpectedly deep divisions (3-5 MYA) among the 3 subspecies tested! #2025MMM www.cell.com/current-biol...
Figure 1 (Janečka et al., 2008). Appearance, distribution & phylogeny of Sunda colugos. (A) Gliding culogo. (B) Geographic distribution of Sunda (green) and Philippine (brown) colugos in Southeast Asia, including locations sampled. (C,D) Maximum likelihood phylogenies reconstructed from mitochondrial (C) and nuclear (D) DNA segments for Sunda colugos, with the Philippine colugo as the outgroup. Branch lengths were estimated under a molecular clock in PAUP* & converted to time based upon an independent molecular calibration point [3] denoted with a blue diamond. The confidence intervals are derived from the upper & lower 95% credibility intervals of the Sunda/Philippine colugo divergence [3]. Taxon labels are colored to correspond with their respective geographic sampling locations in the map.
March 18, 2025 at 12:22 AM