Nathan S. Upham

Arizona State University | ASU · School of Life Sciences

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...

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...

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...

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...

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...

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Non-vertical modes of evolution—such as hybridization/introgression and horizontal gene transfer—deviate from a strictly bifurcating tree model, causing non-treelike patterns. Here, we present a brief overview...

We welcome feedback on the range maps published in Marsh et al. (2022) where it constructively improves our knowledge on species distributions. Unfortunately, we are concerned that criticisms raised by Arbogast and Kerhoulas are steps backward, not forward, particularly as they did not access the original range map data of Marsh et al. (2022). We s...

Raw data and R-code for the research approach on phylogenetic multiple imputation of natural history traits for tetrapod species. In brief, the code computes the phylogenetic filters, reproduces the grid search procedure to tune XGBoost hyperparameters; compute phylogenetic multiple imputations for traits related to body length, body mass, activity...

Please, access the file through its DOI. Version 1.0.0 (19 April 2024). TetrapodTraits, the full phylogenetically coherent database we developed, is being made publicly available to support a range of research applications in ecology, evolution, and conservation and to help minimise the impacts of biassed data in this model system. The database inc...

Phylogenomics has enriched our understanding of the Tree of Life. Non-vertical modes of evolution—such as hybridization/introgression and horizontal gene transfer—deviate from a strictly bifurcating tree model, mirroring a network-like or reticulate structure. Here, we present an overview of a phylogenomic workflow for inferring organismal historie...

Rodentia is the most speciose order of mammals, and they are known to harbor a wide range of viruses. Although there has been significant research on zoonotic viruses in rodents, research on the diversity of other viruses has been limited, especially for rodents in the families Cricetidae and Heteromyidae. In fecal and liver samples of nine species...

We describe a novel dataset for the automated recognition of named taxonomic and other entities relevant to the association of viruses with their hosts. We further describe some initial results using pre-trained models on the named-entity recognition (NER) task on this novel dataset. We propose that our dataset of manually annotated abstracts now o...

Diverse mammal genomes open a new portal to hidden aspects of evolutionary history.

Bats (order Chiroptera) are some of the most abundant mammals on earth and their species ecology strongly influences zoonotic potential. While substantial research has been conducted on bat-associated viruses, particularly on those that can cause disease in humans and/or livestock, globally, limited research has focused on endemic bats in the USA....

Many of Madagascar’s unique species are threatened with extinction. However, the severity of recent and potential extinctions in a global evolutionary context is unquantified. Here, we compile a phylogenetic dataset for the complete non-marine mammalian biota of Madagascar and estimate natural rates of extinction, colonization, and speciation. We m...

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,...

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...

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...

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...

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...

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...

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...

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...

To determine the distribution and causes of extinction threat across functional groups of terrestrial vertebrates, we assembled an ecological trait data set for 18,016 species of terrestrial vertebrates and utilized phylogenetic comparative methods to test which categories of habitat association, mode of locomotion, and feeding mode best predicted...

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...

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...

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...

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...

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...

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...

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...

[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...

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...

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...

“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...

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...

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...

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...

https://www.researchgate.net/deref/https%3A%2F%2Facademic.oup.com%2Fbioscience%2Farticle%2Fdoi%2F10.1093%2Fbiosci%2Fbiaa064%2F5857068

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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.

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...

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)...

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;...

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).

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...

DOI: 10.5710/AMGH.v53i4.1

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...

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...

[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...

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...

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...

The two currently recognized species of kangaroo mice, Microdipodops megacephalus and M. pallidus, inhabit sandy soils of the Great Basin Desert in western North America. Given their habitat specificity and the fluctuating climate throughout the Pleistocene, kangaroo mice likely endured a turbulent biogeographic history that resulted in disjunct di...

Rodents make foraging decisions by balancing demands to acquire energy and mates with the need to avoid predators. To identify variations in the risk of predation, nocturnal rodents may use moonlight as a cue of risk. Moonlight avoidance behaviors have been observed in many nocturnal rodent species and are widely generalized to small mammals. Howev...

The rodent superfamily Octodontoidea comprises 6 families, 38 genera, and 193 living species of spiny rats, tuco-tucos, degus, hutias, and their relatives. All are endemic to the Neotropical Region where they represent roughly three-quarters of extant caviomorphs. Although caviomorph monophyly is well established and phylogenetic hypotheses exist f...

Aim The rodent genus Microdipodops (kangaroo mice) includes two sand-obligate endemics of the Great Basin Desert: M. megacephalus and M. pallidus. The dark kangaroo mouse, M. megacephalus, is distributed throughout the Great Basin and our principal aims were to formulate phylogenetic hypotheses for this taxon and make phylogeographical comparisons...

Aim Kangaroo mice, genus Microdipodops Merriam, are endemic to the Great Basin and include two species: M. pallidus Merriam and M. megacephalus Merriam. The pallid kangaroo mouse, M. pallidus, is a sand-obligate desert rodent. Our principal intent is to identify its current geographical distribution and to formulate a phylogeographical hypothesis f...

Rodents make foraging decisions by balancing energetic and reproductive demands with predator avoidance. To identify variations in the risk of predation, nocturnal rodents may use moonlight as an indirect cue of risk. Moonlight avoidance behaviors have been observed in many nocturnal rodents and are widely generalized to small mammals, but in no pr...

The distribution of kangaroo mice, genus Microdipodops (Rodentia: Heteromyidae ), is limited exclusively to the hydrographic Great Basin region of western North America (Hafner, 1978; 1993).The phylogeography of populations of the Dark Kangaroo Mouse, Microdipodops megacephalus, were examined within this region using mitochondrial DNA (mtDNA) seque...

The distribution of the Dark Kangaroo Mouse, Microdipodops megacephalus (Rodentia: Heteromyidae), is limited exclusively to sandy habitats within the hydrographic Great Basin region of western North America. The phylogeography of populations of M. megacephalus were examined throughout its distribution using mitochondrial DNA (mtDNA) sequence data....