Nathan S. Upham

Nathan S. Upham
Arizona State University | ASU · School of Life Sciences

PhD in Evolutionary Biology
My group studies mammal phylogenetic ecology: Know your species and their history to ask how and why organisms interact.

About

68
Publications
103,273
Reads
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2,094
Citations
Citations since 2016
53 Research Items
1907 Citations
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Introduction
We study biodiversity from a spatial and temporal perspective, integrating data from DNA, fossils, and species traits to investigate when groups of species originated, at what evolutionary rates, and in the context of what ecological interactions. Our research is centered on mammal evolution and has focused on lineages of rats and mice in the tropical Americas (spiny rats, hutias), deserts of North and South America (kangaroo mice and vizcacha rats), and most recently across global Mammalia.
Additional affiliations
April 2015 - February 2020
Yale University
Position
  • PostDoc Position
June 2014 - April 2015
McMaster University
Position
  • PostDoc Position
April 2014 - present
Field Museum of Natural History
Position
  • Research Associate

Publications

Publications (68)
Article
Full-text available
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of species involves numerous trade-offs that have limited their utility to comparative biologists. To establish a robust evolutionary timescale for all approximately 6,000 living...
Article
Full-text available
Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil record or time-calibrated phylogenies (timetrees) of living species. Extinct lineages unsampled in timetrees are known to “pull” s...
Article
Full-text available
Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to lar...
Article
Full-text available
The genome of the red vizcacha rat (Rodentia, Octodontidae, Tympanoctomys barrerae) is the largest of all mammals, and about double the size of their close relative, the mountain vizcacha rat Octomys mimax, even though the lineages that gave rise to these species diverged from each other only about 5 Ma. The mechanism for this rapid genome expansio...
Chapter
Full-text available
The Caviomorpha is a diverse lineage of hystricognath rodents endemic to the Americas and Caribbean islands. We analyzed evolutionary relationships within 11 families of caviomorphs and their relatives in the suborder Ctenohystrica using a supermatrix of 199 taxa and DNA sequences from five genes. New gene sequences were generated for 33 genera, in...
Article
Full-text available
Taxonomy is at the center of modern biodiversity science, since it defines the dual name and meaning of species that jointly allows biologists to study and classify organisms while linking observations from multiple sources. With the accelerating digitization of biodiversity data has come the increased need for readily available taxonomic products,...
Article
Full-text available
Understanding variation of traits within and among species through time and across space is central to many questions in biology. Many resources assemble species-level trait data, but the data and metadata underlying those trait measurements are often not reported. Here, we introduce FuTRES (Functional Trait Resource for Environmental Studies; pron...
Article
Full-text available
Bats harbour a diverse array of viruses, some of which are zoonotic, and are one of the most speciose groups of mammals on earth. As part of an ongoing bat-associated viral diversity research project, we identified three cycloviruses (family Circoviridae) in fecal samples of silver-haired bats (Lasionycteris noctivagans) caught in Cave Creek Canyon...
Article
Full-text available
Taxonomy is at the center of modern biodiversity science. No species can be systematically studied until it is defined, and no observation can be linked to related data without a taxonomic label. However, taxonomy is also a science in constant flux—even well-studied groups like Mammalia have fluctuated by >25% in recognized species in the last deca...
Article
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At least 29% of the world’s terrestrial ecosystems have been significantly modified by human activity (Ellis 2011). Total livestock biomass is 15 times greater than that of wild mammals (Bar-On et al. 2018). Crops such as maize, soybean, rice, and wheat cover 23% of available agricultural land (Ritchie and Roser 2013). Even where land is not farmed...
Preprint
Madagascar's biota has suffered recent extinctions and many of its unique species are threatened. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. We compiled a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimated natural rates of extinction, coloniza...
Article
Full-text available
Ungulate migrations are crucial for maintaining abundant populations and functional ecosystems. However, little is known about how or why migratory behaviour evolved in ungulates. To investigate the evolutionary origins of ungulate migration, we employed phylogenetic path analysis using a comprehensive species-level phylogeny of mammals. We found t...
Article
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Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroeco...
Article
Full-text available
The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns – but whether these factors also contribute to modern extinction risk is lar...
Article
Full-text available
To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled a dataset on ecological traits for 18,016 species and tested, with phylogenetic comparative methods, which categories of habitat association, mode of locomotion, and feeding mode best predict extinction risk. We found that...
Article
Full-text available
Making the most of biodiversity data requires linking observations of biological species from multiple sources both efficiently and accurately (Bisby 2000, Franz et al. 2016). Aggregating occurrence records using taxonomic names and synonyms is computationally efficient but known to experience significant limitations on accuracy when the assumption...
Article
Full-text available
Domestic and captive animals and cultivated plants should be recognised as integral components in contemporary ecosystems. They interact with wild organisms through such mechanisms as hybridization, predation, herbivory, competition and disease transmission and, in many cases, define ecosystem properties. Nevertheless, it is widespread practice for...
Article
Full-text available
The current crisis in global natural resource management makes it imperative that we better leverage the vast data sources associated with taxonomic entities (such as recognized species of plants and animals), which are known collectively as biodiversity data. However, these data pose considerable challenges for artificial intelligence: while growi...
Article
Full-text available
Preventing extinctions requires understanding macroecological patterns of vulnerability or persistence. However, correlates of risk can be nonlinear, within-species risk varies geographically, and current-day threats cannot reveal drivers of past losses. We investigated factors that regulated survival or extinction in Caribbean mammals, which have...
Article
Full-text available
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...
Preprint
Full-text available
Connecting basic data about bats and other potential mammal hosts of SARS-CoV-2 with their ecological context is now critical for understanding the emergence and spread of COVID-19. However, when global lockdown started in March 2020, the world’s bat experts were locked out of their research laboratories, which, in turn, locked up large volumes of...
Article
Full-text available
[revised from pre-print posted on Current Biology's SSRN server: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3761886] Reconstructing the tempo at which biodiversity arose is a fundamental goal of evolutionary biologists, yet the relative merits of evolutionary-rate estimates are debated based on whether they are derived from the fossil rec...
Article
Full-text available
Aim: We test whether geographic variation in length of rodent species’ appendages follows predictions of Allen’s rule—a positive relationship between appendage length and temperature—at a broad taxonomic scale (order Rodentia). We also test if the applicability of this rule varies based on the unit of analysis (species or assemblage), examined appe...
Article
Full-text available
Translating information between the domains of systematics and conservation requires novel information management designs. Such designs should improve interactions across the trading zone between the domains, herein understood as the model according to which knowledge and uncertainty are productively translated in both directions (cf. Collins et al...
Article
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“What is crucial for your ability to communicate with me… pivots on the recipient’s capacity to interpret—to make good inferential sense of the meanings that the declarer is able to send” (Rescher 2000, p148). Conventional approaches to reconciling taxonomic information in biodiversity databases have been based on string matching for unique taxonom...
Article
Full-text available
A deep irony of COVID-19 likely originating from a bat-borne coronavirus (Boni et al. 2020) is that the global lockdown to quell the pandemic also locked up physical access to much basic knowledge regarding bat biology. Digital access to data on the ecology, geography, and taxonomy of potential viral reservoirs, from Southeast Asian horseshoe bats...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
https://www.researchgate.net/deref/https%3A%2F%2Facademic.oup.com%2Fbioscience%2Farticle%2Fdoi%2F10.1093%2Fbiosci%2Fbiaa064%2F5857068
Data
This data publication originated as part of developing a biodiversity-related knowledge hub on COVID-19 via COVID19-TAF - Communities Taking Action (https://cetaf.org/covid19-taf-communities-taking-action), a community-rooted initiative raised jointly by the Consortium of European Taxonomic Facilitaties (CETAF, https://cetaf.org) and Distributed Sy...
Data
This data publication originated as part of developing a biodiversity-related knowledge hub on COVID-19 via COVID19-TAF - Communities Taking Action (https://cetaf.org/covid19-taf-communities-taking-action), a community-rooted initiative raised jointly by the Consortium of European Taxonomic Facilitaties (CETAF, https://cetaf.org) and Distributed Sy...
Article
Full-text available
The Systematic Collections Committee of the American Society of Mammalogists advises curators and other personnel affiliated with natural history collections in matters relating to administration, curation, and accreditation of mammal specimens and their associated data. The Systematic Collections Committee also maintains a list of curatorial stand...
Preprint
Full-text available
The uneven distribution of species in the tree of life is rooted in unequal speciation and extinction among groups. Yet the causes of differential diversification are little known despite their relevance for sustaining biodiversity into the future. Here we investigate rates of species diversification across extant Mammalia, a compelling system that...
Article
Full-text available
As a periodic assessment of the mammal collection resource, the Systematic Collections Committee (SCC) of the American Society of Mammalogists undertakes decadal surveys of the collections held in the Western Hemisphere. The SCC surveyed 429 collections and compiled a directory of 395 active collections containing 5,275,155 catalogued specimens. Ov...
Article
Full-text available
We investigated spatial patterns of evolutionary relatedness and diversification rates to test hypotheses about the historical biogeographic processes underlying the radiation of Neotropical rats and mice (Sigmodontinae, ~400 species). A negative correlation between mean phylogenetic distance and diversification rates of rodent assemblages reveals...
Article
Full-text available
Accurate taxonomy is central to the study of biological diversity, as it provides the needed evolutionary framework for taxon sampling and interpreting results. While the number of recognized species in the class Mammalia has increased through time, tabulation of those increases has relied on the sporadic release of revisionary compendia like the M...
Article
Full-text available
The extensive postglacial mammal losses in the West Indies provide an opportunity to evaluate extinction dynamics, but limited data have hindered our ability to test hypotheses. Here, we analyze the tempo and dynamics of extinction using a novel data set of faunal last-appearance dates and human first-appearance dates, demonstrating widespread over...
Article
Full-text available
The majority (90%) of native terrestrial mammal species living in the Dominican Republic are bats, and two-thirds of these species are endemic to the Caribbean. However, recent molecular studies using DNA barcoding of the mitochondrial cytochrome c oxidase subunit 1 gene have suggested at least a 25% underestimation of biodiversity in bats througho...
Article
Full-text available
The insular radiation of hutias is remarkable among mammals for its high rate of extinction during the Holocene (~58% of species), yet fragments of intact habitat throughout the West Indies retain a critical portion of endemic diversity needing assessment. Cuba contains 8 of the 11 recognized living species of hutias, with surviving forms also on H...
Article
Full-text available
Of the 116 mammal species present in the Greater Antilles at the start of the Holocene Epoch, only 56 now survive, with more extensive species losses (~80%) in native lineages of sloths, shrews, rodents, and primates than in bats (~25%). Native species occurrences and extinctions are summarized herein for Cuba, Hispaniola, Jamaica, and Puerto Rico...
Poster
Full-text available
J.L. Dunnum*, R.C. Dowler, and ASM Systematic Collections Committee (2017): ASM Systematic Collections Committee 2017 resurvey of the mammal collections of the western hemisphere. Poster presented at the 97th Annual Meeting of the American Society of Mammalogists, University of Idaho, Moscow, Idaho, EEUU.
Article
Full-text available
Evolutionary radiations on continents are less well understood and appreciated than those occurring on islands. The extent of ecological influence on species divergence can be evaluated to determine whether a radiation was ultimately the outcome of divergent natural selection or else arose mainly by non-ecological divergence. Here, we used phylogen...
Article
Full-text available
Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae)...
Article
Full-text available
The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009;...
Data
This plot is not part of the published stance but derives from it. The plot shows the number of authors by geographic region (courtesy of Dr. Diego Astua).
Chapter
Full-text available
15 Volume 6 of the Handbook of the Mammals of the World presents a thorough synthesis of the mam-malian clade Glires, consisting of the orders Lagomorpha and Rodentia. The number of species in each of these two orders is in constant flux as new species are described, recognized forms are split into multiple previously cryptic species, and previousl...
Article
Full-text available
Analyses of morphological and molecular data indicate the existence of an unrecognized and unnamed species of soft-haired mouse, genus Abrothrix. Here, we name and describe this new species, which inhabits the Valdivian ecoregion, from the north of Chiloé Island onto the mainland in the Chilean regions of Los Lagos and Los Ríos; it also occurs at a...
Article
Full-text available
The Ctenohystrica is one of the three major lineages of rodents and contains diverse forms related to gundis, por-cupines, and guinea pigs. Phylogenetic analyses of this group using mitochondrial and nuclear gene sequences confirm the monophyly of the infraorder Hystricognathi and most of its recognized subclades, including both the Neotropical cav...
Article
Full-text available
[Open Access article: http://journal.frontiersin.org/Journal/10.3389/fevo.2014.00044/full] Lessa et al. (2014) make a compelling case for systematic exploration of genomes in the diverse South American rodent fauna. Not only do the caviomorph and sigmod-ontine rodents comprise a sizable portion of the continental fauna, but they have radiated into...
Thesis
Full-text available
A major topic in evolutionary biology concerns the process of biological diversification. The cosmopolitan order Rodentia is the most diverse mammalian radiation with ca. 2300 living species, or about 40% of all mammals. The Caviomorpha, best known from the domesticated guinea pig (Cavia), was the first rodent lineage to reach South America. Their...
Article
Full-text available
The tropical Andes and Amazon are among the richest regions of endemism for mammals, and each has given rise to extensive in situ radiations. Various animal lineages have radiated ex situ after colonizing one of these regions from the other: Amazonian clades of dendrobatid frogs and passerine birds may have Andean ancestry, and transitions from the...