Cody W . Thompson | University of Michigan (original) (raw)

Papers by Cody W . Thompson

$Research paper thumbnail of \u3ci\u3eBlarina hylophaga\u3c/i\u3e (Sorciomorpha: Soricidae)$

Blarina hylophaga (Elliot, 1899) is a soricid commonly called Elliot’s short-tailed shrew. A shor... more Blarina hylophaga (Elliot, 1899) is a soricid commonly called Elliot’s short-tailed shrew. A short-legged, robust shrew with a long, pointed snout and a short tail; it is 1 of 4 species in the genus Blarina. It occurs throughout most of the Great Plains of the United States, where it inhabits moist, well-drained grassland and riparian areas with deep leaf litter. It is listed as a species of greatest conservation need in Iowa and at possible risk in Texas, which might be due to the limited knowledge of the species throughout its geographic range

Multilocus analyses indicate a mosaic distribution of hybrid

PLOS Pathogens, 2021

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in ... more The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emerging pathogens and their reservoir host(s) and precludes extended investigation of ecological, evolutionary, and environmental associations that lead to human infection or spillover. Natural history museum biorepositories form the backbone of a critically needed, decentralized, global network for zoonotic pathogen surveillance, yet this infrastructure remains marginally developed, underutilized, underfunded, and disconnected from public health initiatives. Proactive detection and mitigation for emerging infectious diseases (EIDs) requires expanded biodiversity infrastructure and training (particularly in biodiverse and lower income countri...

Science, 2020

Decade-old (1) and recent warnings for coronaviruses with zoonotic epidemic potential (2) could h... more Decade-old (1) and recent warnings for coronaviruses with zoonotic epidemic potential (2) could have prevented the emergence of coronavirus disease 2019 (COVID-19) (3). We therefore agree with Watsa and colleagues ("Rigorous wildlife disease surveillance," Perspective, 10 July, p. 145) that wildlife biosurveillance should increase. However, representing animals as a threat to humans through disease transmission leads to ill-conceived reactive policies (4). A perspective (5) in which animals and humans share similar risks of pathogens and infections, making animals relevant disease models and sentinels, would be more effective. Clarifying the connection between animal and human health could increase public support for research seeking to understand host-switching in animals, such as the study of virus evolution (6), interactions in pathogen communities (7), and pathogen discovery (8). A shared-risk perspective on emerging infectious diseases mirrors the field of EcoHealth, which explores the links between ecosystem, animal, and human health. Such strategies place value in healthy ecosystems through an integrative LETTERS approach that considers both pathogen biodiversity and social-ecological drivers (9). Prevention based on understanding the transmission of pathogens through EcoHealth-based emerging infectious disease surveillance is a promising avenue for sustainability science, orders of magnitude cheaper than mitigation in response to a transfer to human hosts (10), and less intrusive than current crisis responses.

Journal of Mammalogy, 2019

A taxonomic framework for South American cottontail rabbits (Lagomorpha: Leporidae: Sylvilagus) w... more A taxonomic framework for South American cottontail rabbits (Lagomorpha: Leporidae: Sylvilagus) was recently published by Diersing and Wilson (2017). Although we agree with some of its taxonomic conclusions (e.g., species status for S. apollinaris and S. fulvescens), we disagree with others. We provide herein evidence supporting S. andinus as a valid species based on morphological characters and novel molecular data. We also provide details of the morphological characters of S. apollinaris and S. fulvescens that support separating these from S. brasiliensis. We adduce data suggestive to the effect that—absent any type material—S. defilippi is at best a nomen dubium. Finally, we provide evidence in support of recognizing additional Neotropical species of Sylvilagus.Un esquema taxonómico para los conejos sudamericanos (Lagomorpha: Leporidae: Sylvilagus) fue recientemente publicado por Diersing y Wilson (2017). Aunque estamos de acuerdo con algunas de sus conclusiones (por ejemplo: est...

DNA sequences from the interphotoreceptor retinoid binding protein gene (Rbp3) in pocket gophers ... more DNA sequences from the interphotoreceptor retinoid binding protein gene (Rbp3) in pocket gophers (Geomys) display an unusually slow rate of molecular evolution relative to other species of rodents. Rates of molecular evolution were examined in pocket gophers and other members of the rodent superfamily Geomyoidea to determine if this phenomenon was restricted to pocket gophers. DNA sequences from the Rbp3, mitochondrial 12S ribosomal RNA (12S rRNA), and mitochondrial cytochrome-b (Cytb) genes were compared within members of Geomys, among members of the Geomyidae, and among members of the Geomyoidea to ascertain rates of molecular evolution for the three genes among the various taxa. A variety of analyses (genetic distance, Tajima's relative rate test, Tajima's neutrality test, coalescence theory, and Hudson, Kreitman, and Aguadé test) indicated that DNA sequences affiliated with Rbp3 in species of Geomys were evolving at a rate slower than were sequences of members of the Heteromyidae. In addition, there was weak evidence suggesting that the Rbp3 gene in other pocket gopher genera (Cratogeomys, Orthogeomys, Pappogeomys, and Thomomys) evolved more slowly than in members of the Heteromyidae.

Journal of Mammalogy, 2018

Journal of Mammalogy, 2015

The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon,... more The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.

Zoology Via L. da Vinci 44, 10095 Grugliasco (TO), Italy 4 Lurzengasse 3, D-97236 Randersacker, G... more Zoology Via L. da Vinci 44, 10095 Grugliasco (TO), Italy 4 Lurzengasse 3, D-97236 Randersacker, Germany 5 Wildlife Conservation and Management, School of Natural Resources and the Environment, 306 Biological Sciences East, Abstract The eastern gray squirrel, Sciurus carolinensis, is one of the world's most recognized sciurids and a highly successful human commensal. Historically restricted to eastern North America, gray squirrel populations are now established in Italy, U.K., South Africa, and Australia, and squirrels continue to expand their geographic range globally. Successful introductions of S. carolinensis often result in significant negative impacts on native ecosystem integrity. As a result, countries have devised and implemented unique pest management strategies to reduce or eradicate S. carolinensis populations, but with differing levels of success. We review accounts of historical global introductions of S. carolinensis, discuss its invasive biology and impacts in non...

Ecology and Evolution, 2013

DNA sequence data from mitochondrial cytochrome-b (Cytb) and Y-linked structural maintenance of c... more DNA sequence data from mitochondrial cytochrome-b (Cytb) and Y-linked structural maintenance of chromosomes (SmcY) genes were combined with 478 nuclear loci obtained from amplified fragment length polymorphisms (AFLP) to assess the extent of hybridization and genetic spatial structure of populations in two hybridizing species of ground squirrel (Ictidomys parvidens and Ictidomys tridecemlineatus). Based on AFLP analyses of 134 individuals from 28 populations, 10 populations were identified that possessed hybrid individuals. Overall estimates of F ST values revealed strong support for population structure in the Cytb data set; however, analyses of the SmcY gene and the AFLP data indicated ongoing gene flow between species. Pairwise F ST comparisons of populations were not significant for the SmcY gene; although they were significant for the Cytb gene, indicating that these populations were structured and that gene flow was minimal. Therefore, gene flow between I. parvidens and I. tridecemlineatus appeared to be restricted to populations that exhibited hybridization. In addition, the fragmented nature of the geographic landscape suggested limited gene flow between populations. As a result, the distributional pattern of interspersed parental and hybrid populations were compatible with a mosaic hybrid zone model. Because ground squirrels display female philopatry and male-biased dispersal, the ecology of these species is compatible with this hypothesis.

The Southwestern Naturalist, 2013

Proceedings of the Biological Society of Washington, 2014

Analyses of the mitochondrial cytochrome-b gene were used to determine levels of genetic differen... more Analyses of the mitochondrial cytochrome-b gene were used to determine levels of genetic differentiation and patterns of relationship among members of the Neotoma mexicana (Mexican woodrat) species group in Mesoamerica. Three well-supported clades were obtained that conform to the species N. ferruginea Tomes, 1862, N. mexicana Baird, 1855, and N. picta Goldman, 1904. Neotoma ferruginea is the senior name for the clade that contains samples from southern Mexico and Nuclear Central America previously identified as N. isthmica Goldman, 1904, or as subspecies of N. mexicana (chamula Goldman, 1909; vulcani Sanborn, 1935). The phylogeographic pattern observed within the N. mexicana species group resembles that reported for other vertebrates co-distributed in mountains to the west (Trans-Mexican Neovolcanic Belt, Oaxacan sierras) and east (highlands of Chiapas, Mexico, and Nuclear Central America) of the Isthmus of Tehuantepec. Resumen.-Ana´lisis filogenéticos del gen mitocondrial Citocromo b se utilizaron para determinar los niveles de diferenciación genética y los patrones de relaciones entre miembros del grupo de especies de Neotoma mexicana en Mesoamerica. Se obtuvieron tres clados bien soportandos que esta´n conformados por las especies Neotoma ferruginea Tomes, 1862; N. mexicana Baird, 1855; y N. picta Goldman, 1904. Neotoma ferruginea es el nombre ma´s antiguo para el clado que contiene muestras del sur de México y Centro América Nuclear que previamente fueron identificadas como N. isthmica Goldman, 1904, y una subespecie de N. mexicana (chamula Goldman, 1909; vulcani Sanborn, 1935). El patrón filogeogra´fico observado entre el grupo de especies de N. mexicana se asemeja al reportado para otros vertebrados codistribuidos en las montañas del Oeste (Eje neovolca´nico transversal, Sierras

Western North American Naturalist, 2013

Mammalian Species, 2011

Blarina hylophaga (Elliot, 1899) is a soricid commonly called Elliot 's short-tailed shrew. A sho... more Blarina hylophaga (Elliot, 1899) is a soricid commonly called Elliot 's short-tailed shrew. A short-legged, robust shrew with a long, pointed snout and a short tail; it is I of 4 species in the genus Blarina. It occurs throughout most of the Great Plains of the United States, where it inhabits moist, well-drained grassland and riparian areas with deep leaflitter. It is listed as a species of greatest conservation need in Iowa and at possible risk in Texas, which might be due to the limited knowledge of the species throughout its geographic range .

Canadian Journal of Zoology, 2011

Short-tailed shrews (genus Blarina Gray, 1838) are characterized by divergent karyotypes and are ... more Short-tailed shrews (genus Blarina Gray, 1838) are characterized by divergent karyotypes and are genetically distinct. Blarina species are similar morphologically but, in most cases, can be distinguished morphometrically. Blarina distributions tend to be parapatric along well-defined contact zones; however, it has been suggested that the northern short-tailed shrew ( Blarina brevicauda (Say, 1823)) and Elliot’s short-tailed shrew ( Blarina hylophaga Elliot, 1899) occur sympatrically in Iowa and Missouri. To evaluate this possibility, 179 specimens were collected in southwestern Iowa and northwestern Missouri. Karyotypes and total length were used for field identification, and amplified fragment length polymorphism (AFLP) analysis was used to verify field identifications and to investigate the extent of hybridization. One hundred seventy-eight of 179 specimens were identified to species. The one exception had a karyotype of B. brevicauda (2n = 50, FN = 48); however, AFLP analysis ind...

... tailed shrew (B. hylophaga), which are similar to B. brevicauda in external and cranial morph... more ... tailed shrew (B. hylophaga), which are similar to B. brevicauda in external and cranial morphology (benedict 1999a, 1999b; bowles 1975, 1977; brant and Ortí 2002; braun and Kennedy 1983; Ellis et al. 1978; Genoways and choate 1972; Graham and Semken 1976; Jones et al ...

A NORTHWARD RANGE EXTENSION OF THE HIS-PID COTTON RAT (SIGMODON HISPIDUS) IN MIS-SOURI-The hispid... more A NORTHWARD RANGE EXTENSION OF THE HIS-PID COTTON RAT (SIGMODON HISPIDUS) IN MIS-SOURI-The hispid cotton rat (Sigmodon hispidus) is a widely distributed rodent with a geographic range extending from north-central Mexico to southern Nebraska and central Virginia and from southeastern Arizona east to Florida (Carleton et al. 1999, Peppers and Bradley 2000, Wilson and Reeder 2005) with isolated populations in Arizona (Bradley et al. 2012) and California (Clark 1972). Range expansions for the species have been well documented (Clark 1972, Farney 1975, Benedict et al. 2000, Wright et al. 2010, Wills et al. 2011). The majority of these range expansions have occurred across the Central Plains during the 20 th century and have been attributed to climate change (e.g., Benedict et al. 2000, Hoffman 2008). Bailey (1902) was the first to document movement of S. hispidus into the Central Plains by documenting individuals for the first time in Kansas that most likely moved northward from Oklahoma. By 1947, the species had reached the Kansas/Nebraska border (Cockrum 1948). Just over 10 years later, Jones (1960) reported 12 individuals near the Nemaha River in southeastern Nebraska, and by the late 1960s (Choate and Genoways 1967, Genoways and Schlitter 1967) and mid-1970s (Farney 1975), the species had been documented in several parts of the state. Recent studies have not documented S. hipsidus north of the Platte River in Nebraska (Benedict et al. 2000, Wright et al. 2010, Wills et al. 2011), which may have acted as a