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Paxton KL, Cassin-Sackett L, Atkinson CT, Videvall E, Campana MG, Fleischer RC. Gene expression reveals immune response strategies of naïve Hawaiian honeycreepers experimentally infected with introduced avian malaria. J Hered 2023; 114:326-340. [PMID: 36869776 DOI: 10.1093/jhered/esad017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/01/2023] [Indexed: 03/05/2023] Open
Abstract
The unprecedented rise in the number of new and emerging infectious diseases in the last quarter century poses direct threats to human and wildlife health. The introduction to the Hawaiian archipelago of Plasmodium relictum and the mosquito vector that transmits the parasite has led to dramatic losses in endemic Hawaiian forest bird species. Understanding how mechanisms of disease immunity to avian malaria may evolve is critical as climate change facilitates increased disease transmission to high elevation habitats where malaria transmission has historically been low and the majority of the remaining extant Hawaiian forest bird species now reside. Here, we compare the transcriptomic profiles of highly susceptible Hawai'i 'amakihi (Chlorodrepanis virens) experimentally infected with P. relictum to those of uninfected control birds from a naïve high elevation population. We examined changes in gene expression profiles at different stages of infection to provide an in-depth characterization of the molecular pathways contributing to survival or mortality in these birds. We show that the timing and magnitude of the innate and adaptive immune response differed substantially between individuals that survived and those that succumbed to infection, and likely contributed to the observed variation in survival. These results lay the foundation for developing gene-based conservation strategies for Hawaiian honeycreepers by identifying candidate genes and cellular pathways involved in the pathogen response that correlate with a bird's ability to recover from malaria infection.
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Affiliation(s)
- Kristina L Paxton
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Hawai'i Cooperative Studies Unit, University of Hawai'i Hilo, PO Box 44, Hawai'i National Park, HI 96718, USA
| | - Loren Cassin-Sackett
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Department of Biology, University of Louisiana, Lafayette, LA 70503, USA
| | - Carter T Atkinson
- U.S. Geological Survey Pacific Island Ecosystems Research Center, PO Box 44, Hawai'i National Park, HI 96718, USA
| | - Elin Videvall
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
- Department of Ecology, Evolution and Organismal Biology, Brown University, Providence, RI 02912, USA
| | - Michael G Campana
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, National Zoological Park and Conservation Biology Institute, Smithsonian Institution, Washington, DC 20008, USA
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2
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Nilsson P, Ravinet M, Cui Y, Berg PR, Zhang Y, Guo R, Luo T, Song Y, Trucchi E, Hoff SNK, Lv R, Schmid BV, Easterday WR, Jakobsen KS, Stenseth NC, Yang R, Jentoft S. Polygenic plague resistance in the great gerbil uncovered by population sequencing. PNAS NEXUS 2022; 1:pgac211. [PMID: 36712379 PMCID: PMC9802093 DOI: 10.1093/pnasnexus/pgac211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 06/18/2023]
Abstract
Pathogens can elicit high selective pressure on hosts, potentially altering genetic diversity over short evolutionary timescales. Intraspecific variation in immune response is observable as variable survivability from specific infections. The great gerbil (Rhombomys opimus) is a rodent plague host with a heterogenic but highly resistant phenotype. Here, we investigate the genomic basis for plague-resistant phenotypes by exposing wild-caught great gerbils to plague (Yersinia pestis). Whole genome sequencing of 10 survivors and 10 moribund individuals revealed a subset of genomic regions showing elevated differentiation. Gene ontology analysis of candidate genes in these regions demonstrated enrichment of genes directly involved in immune functions, cellular metabolism and the regulation of apoptosis as well as pathways involved in transcription, translation, and gene regulation. Transcriptomic analysis revealed that the early activated great gerbil immune response to plague consisted of classical components of the innate immune system. Our approach combining challenge experiments with transcriptomics and population level sequencing, provides new insight into the genetic background of plague-resistance and confirms its complex nature, most likely involving multiple genes and pathways of both the immune system and regulation of basic cellular functions.
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Affiliation(s)
- Pernille Nilsson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | | | | | | | | | - Rong Guo
- Xinjiang Center for Disease Control and Prevention, Urumqi 830002, China
| | - Tao Luo
- Xinjiang Center for Disease Control and Prevention, Urumqi 830002, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy
| | - Siv N K Hoff
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | - W Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, 0371 Oslo, Norway
| | | | | | - Ruifu Yang
- To whom correspondence should be addressed:
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3
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Kaufmann C, Cassin-Sackett L. Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.758348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.
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Tsuchiya MTN, Dikow RB, Cassin-Sackett L. First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague. Genome Biol Evol 2021; 12:618-625. [PMID: 32277812 PMCID: PMC7250503 DOI: 10.1093/gbe/evaa069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2020] [Indexed: 12/30/2022] Open
Abstract
Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America's grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison's prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels.
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Affiliation(s)
- Mirian T N Tsuchiya
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
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5
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Joubran SS, Cassin-Sackett L. Genomic resources for an ecologically important rodent, Gunnison’s prairie dogs (Cynomys gunnisoni). CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01192-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Dennis P, Shuster SM, Slobodchikoff CN. Dialects in the alarm calls of black- tailed prairie dogs (Cynomys ludovicianus): A case of cultural diffusion? Behav Processes 2020; 181:104243. [PMID: 32941980 DOI: 10.1016/j.beproc.2020.104243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 10/23/2022]
Abstract
Prairie dogs (Cynomys spp.) produce an alarm call when a predator appears. Gunnison's prairie dogs (Cynomys gunnisoni) produce calls that vary in spectral structure according to predator type and specific characteristics unique to the individual predator, such as color and shape. These calls vary depending on geographic location and have been characterized as dialects. Black-tailed prairie dogs (Cynomys ludovicianus) also encode information about terrestrial predators in their alarm calls. However, nothing is known about whether there are dialects in these alarm calls, and if so, why these dialects might have arisen. We studied the alarm calls and habitat characteristics of eight different black-tailed prairie dog colonies within the Southwestern USA: Maxwell National Wildlife Refuge, NM, Vermejo Park Ranch, NM, Kiowa National Grasslands, NM, Rita Blanca National Grasslands, TX, and Comanche National Grasslands, CO. An analysis of time and frequency changes in alarm calls showed that colony sites that were located within 30 km each other did not have significant differences in alarm call structure, but sites that were more distant were significantly different from the other sites, consistent with the existence of dialects as well as with genetic models of isolation by distance. The acoustic structure of the alarm calls was not explained by differences in habitat characteristics at each site. A comparison of Squared Euclidian Distances (D2) of alarm calls versus linear distances between sites showed a significant positive correlation, implying that alarm call dialect differences increase the farther one site is from another. This relationship is consistent with a cultural diffusion model of dialects, and is similar to that observed in human dialects.
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Affiliation(s)
- Patricia Dennis
- Department of Biological Sciences, Northern Arizona University, Flagstaff, 86011, United States
| | - Stephen M Shuster
- Department of Biological Sciences, Northern Arizona University, Flagstaff, 86011, United States
| | - C N Slobodchikoff
- Department of Biological Sciences, Northern Arizona University, Flagstaff, 86011, United States.
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Russell RE, Tripp DW, Rocke TE. Differential plague susceptibility in species and populations of prairie dogs. Ecol Evol 2019; 9:11962-11971. [PMID: 31695901 PMCID: PMC6822031 DOI: 10.1002/ece3.5684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 11/24/2022] Open
Abstract
Laboratory trials conducted over the past decade at U.S. Geological Survey National Wildlife Health Center indicate that wild populations of prairie dogs (Cynomys spp.) display different degrees of susceptibility to experimental challenge with fully virulent Yersinia pestis, the causative agent of plague. We evaluated patterns in prairie dog susceptibility to plague to determine whether the historical occurrence of plague at location of capture was related to survival times of prairie dogs challenged with Y. pestis. We found that black-tailed prairie dogs (Cynomys ludovicianus) from South Dakota (captured prior to the detection of plague in the state), Gunnison's prairie dogs (Cynomys gunnisoni) from Colorado, and Utah prairie dogs (Cynomys parvidens) from Utah were most susceptible to plague. Though the susceptibility of black-tailed prairie dogs in South Dakota compared with western locations supports our hypothesis regarding historical exposure, both Colorado and Utah prairie dogs have a long history of exposure to plague. It is possible that for these populations, genetic isolation/bottle necks have made them more susceptible to plague outbreaks.
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Affiliation(s)
- Robin E. Russell
- National Wildlife Health CenterU.S. Geological SurveyMadisonWIUSA
| | - Daniel W. Tripp
- Wildlife Health ProgramColorado Parks and WildlifeFort CollinsCOUSA
| | - Tonie E. Rocke
- National Wildlife Health CenterU.S. Geological SurveyMadisonWIUSA
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8
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Cassin Sackett L. Does the host matter? Variable influence of host traits on parasitism rates. Int J Parasitol 2018; 48:27-39. [DOI: 10.1016/j.ijpara.2017.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/28/2017] [Accepted: 07/03/2017] [Indexed: 11/28/2022]
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9
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Cobble KR, Califf KJ, Stone NE, Shuey MM, Birdsell DN, Colman RE, Schupp JM, Aziz M, Van Andel R, Rocke TE, Wagner DM, Busch JD. Genetic variation at the MHC DRB1 locus is similar across Gunnison's prairie dog (Cynomys gunnisoni) colonies regardless of plague history. Ecol Evol 2016; 6:2624-51. [PMID: 27066243 PMCID: PMC4798151 DOI: 10.1002/ece3.2077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 01/16/2023] Open
Abstract
Yersinia pestis was introduced to North America around 1900 and leads to nearly 100% mortality in prairie dog (Cynomys spp.) colonies during epizootic events, which suggests this pathogen may exert a strong selective force. We characterized genetic diversity at an MHC class II locus (DRB1) in Gunnison's prairie dog (C. gunnisoni) and quantified population genetic structure at the DRB1 versus 12 microsatellite loci in three large Arizona colonies. Two colonies, Seligman (SE) and Espee Ranch (ES), have experienced multiple plague‐related die‐offs in recent years, whereas plague has never been documented at Aubrey Valley (AV). We found fairly low allelic diversity at the DRB1 locus, with one allele (DRB1*01) at high frequency (0.67–0.87) in all colonies. Two other DRB1 alleles appear to be trans‐species polymorphisms shared with the black‐tailed prairie dog (C. ludovicianus), indicating that these alleles have been maintained across evolutionary time frames. Estimates of genetic differentiation were generally lower at the MHC locus (FST = 0.033) than at microsatellite markers (FST = 0.098). The reduced differentiation at DRB1 may indicate that selection has been important for shaping variation at MHC loci, regardless of the presence or absence of plague in recent decades. However, genetic drift has probably also influenced the DRB1 locus because its level of differentiation was not different from that of microsatellites in an FST outlier analysis. We then compared specific MHC alleles to plague survivorship in 60 C. gunnisoni that had been experimentally infected with Y. pestis. We found that survival was greater in individuals that carried at least one copy of the most common allele (DRB1*01) compared to those that did not (60% vs. 20%). Although the sample sizes of these two groups were unbalanced, this result suggests the possibility that this MHC class II locus, or a nearby linked gene, could play a role in plague survival.
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Affiliation(s)
- Kacy R Cobble
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Katy J Califf
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Nathan E Stone
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Megan M Shuey
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Dawn N Birdsell
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Rebecca E Colman
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - James M Schupp
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Maliha Aziz
- Translational Genomics Research Institute North 3051 W. Shamrell Blvd #106 Flagstaff Arizona 86001 USA
| | - Roger Van Andel
- University of California Berkeley MC 7150 Berkeley California 94720 USA
| | - Tonie E Rocke
- United States Geological Survey National Wildlife Health Center 6006 Schroeder Road Madison Wisconsin 53711 USA
| | - David M Wagner
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
| | - Joseph D Busch
- Center for Microbial Genetics and Genomics Northern Arizona University PO Box 4073 Flagstaff Arizona 86011 USA
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Castellanos-Morales G, Ortega J, Castillo-Gámez RA, Sackett LC, Eguiarte LE. Genetic Variation and Structure in Contrasting Geographic Distributions: Widespread Versus Restricted Black-Tailed Prairie Dogs (SubgenusCynomys). J Hered 2015; 106 Suppl 1:478-90. [DOI: 10.1093/jhered/esv021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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11
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Lane-deGraaf KE, Amish SJ, Gardipee F, Jolles A, Luikart G, Ezenwa VO. Signatures of natural and unnatural selection: evidence from an immune system gene in African buffalo. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0658-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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