Data from: Molecular and niche modeling approaches to identify potential amplifying hosts for an emerging tick-borne pathogen, Rickettsia rickettsii subsp. californica, the causative agent of Pacific Coast tick fever
Data files
Dec 06, 2024 version files 473.58 KB
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allticks_thinned_v2.csv
13.35 KB
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Lepus_californicus_thinned.csv
29.79 KB
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Neotoma_fuscipes_thinned.csv
273.71 KB
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Otospermophilus_beecheyi_thinned.csv
6.34 KB
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README.md
9.92 KB
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Sceloporus_occidentalis_thinned.csv
80.11 KB
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Sylvilagus_audubonii_thinned.csv
6.92 KB
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Sylvilagus_bachmanii_Thinned.csv
9.64 KB
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Tamiasciurus_douglasii_thinned.csv
3.14 KB
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ticks_ENMs.R
40.66 KB
Abstract
Pacific Coast tick fever (PCTF) is a recently described zoonotic disease in California caused by a spotted fever group rickettsia (SFGR), Rickettsia rickettsii subsp. californica (formerly Rickettsia 364D) and transmitted by the Pacific Coast tick, Dermacentor occidentalis. Like many emerging vector-borne diseases, knowledge regarding the transmission cycle, contribution from potential amplifying hosts, and geographic distribution of R. rickettsii californica is limited. We paired molecular analysis with comparative spatial niche modeling to identify vertebrate hosts potentially involved the transmission cycle of this pathogen. We identified R. rickettsii californica DNA in three mammal species (Otospermophilus beecheyi, Lepus californicus, and Sylvilagus audubonii). This is the first record of R. rickettsii californica detected in mammals and may indicate potential amplifying hosts for this human pathogen. Species niche modeling of uninfected and infected D. occidentalis identified areas of high suitability along the coast and Sierra Nevada foothills of California. These findings support the hypothesis that amplifying host(s) may support higher infection prevalence in the infected tick regions compared to other parts of the tick’s range. Potential host species distribution models (SDM) were constructed from museum records and niche overlap statistics were used to compare habitat suitability with R. rickettsii californica-infected tick SDMs. We found higher than null overlap of infected ticks with California ground squirrels (O. beecheyii) and trending, but non-significant, overlap with two lagomorph species. Pairing molecular and niche modeling may be a useful approach to identify species that are involved in the maintenance of emerging tick-borne zoonoses.
README: Molecular and niche modeling approaches to identify potential amplifying hosts for an emerging tick-borne pathogen Rickettsia rickettsia subsp. californica, the causative agent of Pacific Coast Tick Fever
https://doi.org/10.5061/dryad.7wm37pw1z
Description of the data and file structure
"ticks_ENMs" R script in .R format to be used in R or RStudio. Script includes all necessary packages and instructions to set up analyses for species distribution modeling, load environmental variables, and to run background tests. Code for running models for all Dermacentor occidentalis ticks as well as ticks infected with Rickettsia rickettsii subsp. californica are included. Script is included for modeling the species distribution for all potential host species including Lepus californicus, Sylvilagua bachmani, Sylvilagus audubonii, Otospermophilus beecheyi, Neotoma fuscipes, Tamiasciurus douglasii, Peromyscus maniculatus, P. boylii, P. californicus, and Sceloporus occidentalis. Script for niche comparison between infected ticks and three focus hosts species is also included.
"Lepus californicus thinned.csv" dataset downloaded from VertNet (www.vertnet.org) and spatially thinned for all California occurrences of L. californicus. Data fields include "name": species name, occurrence "longitude" and "latitude", "bibliographiccitation": museum source and record number, "institutioncode": code of institution holding the collection, "collectioncode": the category of collection, "basisofrecord": indicating specimen type, "occurenceid": showing collection identification number, "catalognumber": catalog number at the holding institution, "recordnumber": collection record number, "sex": specimen sex, "eventdate": date of collection, "stateprovince": state of collection, "county": county of collection, "locality": more specific locality details, "scientificname": full scientific name of specimen, and "occID": the internal identifier given to the sample. Missing data or not applicable data are indicated by "NA".
"Neotoma fuscipes thinned.csv" dataset downloaded from VertNet (www.vertnet.org) and spatially thinned for all California occurrences. Data fields include "name": species name, occurrence "longitude" and "latitude", "bibliographiccitation": museum source and record number, "institutioncode": code of institution holding the collection, "collectioncode": the category of collection, "occurenceid": showing collection identification number, "sex": specimen sex, "eventdate": date of collection, "stateprovince": state of collection, "county": county of collection, "locality": more specific locality details. Missing data or not applicable data are indicated by "NA".
"Otospermophilus beecheyi thinned.csv" dataset downloaded from VertNet (www.vertnet.org) and spatially thinned for all California occurrences. Data fields include "name": species name, occurrence "longitude" and "latitude", "institutioncode": code of institution holding the collection, "basisofrecord": indicating specimen type, "occurenceid": showing collection identification number, "catalognumber": catalog number at the holding institution, "recordnumber": collection record number, "sex": specimen sex, "eventdate": date of collection, "county": county of collection, "locality": more specific locality details, "infraspecific epithet": subspecies name. Missing data or not applicable data are indicated by "NA".
"Sceloporus occidentalis thinned.csv" dataset downloaded from VertNet (www.vertnet.org) and spatially thinned for all California occurrences. Data fields include "name": species name, occurrence "longitude" and "latitude", "bibliographiccitation": museum source and record number, "institutioncode": code of institution holding the collection, "collectioncode": the category of collection, "basisofrecord": indicating specimen type, "occurenceid": showing collection identification number, "occurrenceid": full collection identifier, "catalognumber": catalog number at the holding institution, "recordnumber": collection record number, "sex": specimen sex, "lifestage": specimen life stage, "preparations": type of specimen preservation, "eventdate": date of collection, "stateprovince": state of collection, "county": county of collection, "locality": more specific locality details, "scientificname": full scientific name of specimen, and "occID": the internal identifier given to the sample. Missing data or not applicable data are indicated by "NA".
"Sylvilagus audubonii thinned.csv" dataset downloaded from VertNet (www.vertnet.org) and spatially thinned for all California occurrences. Data fields include "name": species name, occurrence "longitude" and "latitude", "MammalID": identification number of specimen, "ID": institutional catalog number of specimen, "CollectionDate": date of specimen collection, "County": county of collection, "Institutioncode": code of institution holding the collection, and "occID": the internal identifier given to the sample. Missing data or not applicable data are indicated by "NA".
"Sylvilagus bachmanii thinned.csv" dataset downloaded from VertNet (www.vertnet.org) and spatially thinned for all California occurrences. Data fields include "name": species name, occurrence "longitude" and "latitude", "county": county of collection, "eventdate": date of collection, "institutioncode": code of institution holding the collection, "collectioncode": the category of collection, "basisofrecord": indicating specimen type, "occurenceid": showing collection identification number, "catalognumber": catalog number at the holding institution, and "occID": the internal identifier given to the sample. Missing data or not applicable data are indicated by "NA".
"Tamiasciurus douglasii thinned.csv" dataset downloaded from VertNet (www.vertnet.org) and spatially thinned for all California occurrences. Data fields include "name": species name, occurrence "longitude" and "latitude", "Mammal.ID": identifying number of specimen, "Collection.Date": date of specimen collection, "County": county of collection, "Institutioncode": code of institution holding the specimen, and "occID": the internal identifier given to the sample. Missing data or not applicable data are indicated by "NA".
"allticks_thinned v2.csv" dataset of spatially thinned occurrence data. Datasource: compiled from California Department of Public Health data and published localities in Padgett et al. 2016, Paddock et al. 2018, and Paddock et al. 2024. Data fields include "name": species name, "longitude": collection longitude, "latitude" collection latitude, "Tick.ID": tick ID if available, "Collection.Date": date of specimen collection, "County": county of collection in California, "Site": specific site name if available, "Life.Stage": tick life stage, "Sex": tick sex if available, "364D.infection.status: tick infection status with Rickettsia rickettsii californica as a binary with "1" indicating infected and "0" indicating uninfected, "Assay": molecular assay used to determine infection status with R. rickettsii californica, "Source": tick occurence and infection data source, "occID": specimen identification number. Missing data or not applicable data are indicated by "NA".
Padgett KA, Bonilla D, Eremeeva ME, et al. 2016. The Eco-epidemiology of Pacific Coast tick fever in California. PLOS Negl. Trop. Dis. 10(10), e0005020. https://doi.org/10.1371/journal.pntd.0005020
Paddock CD, Yoshimizu MH, Zambrano ML, et al. 2018. Rickettsia species isolated from Dermacentor occidentalis (Acari: Ixodidae) from California. J. Med. Entom. 55(6), 1555–1560. https://doi.org/10.1093/jme/tjy100
Paddock CD, Zambrano ML, Clover JR, et al. 2024. Rickettsia species identified in adult, host-seeking Dermacentor occidentalis (Acari: Ixodidae) from Baja California, Mexico, and Oregon and Washington, USA. J. Med. Entomol. 61, 781-90.
Further methodological details are provided in Mai et al. 2024 J. of Medical Entomology.
Sharing/Access information
Links to other publicly accessible locations of the data:
California Department of Public Health data on tick borne diseases
Additional Dermacentor occidentalis occurrence and infection data was derived from the following sources:
- Padgett KA, Bonilla D, Eremeeva ME, et al. 2016. The Eco-epidemiology of Pacific Coast tick fever in California. PLOS Negl. Trop. Dis. 10(10), e0005020. https://doi.org/10.1371/journal.pntd.0005020
- Paddock CD, Yoshimizu MH, Zambrano ML, et al. 2018. Rickettsia species isolated from Dermacentor occidentalis (Acari: Ixodidae) from California. J. Med. Entom. 55(6), 1555–1560. https://doi.org/10.1093/jme/tjy100
- Paddock CD, Zambrano ML, Clover JR, et al. 2024. Rickettsia species identified in adult, host-seeking Dermacentor occidentalis (Acari: Ixodidae) from Baja California, Mexico, and Oregon and Washington, USA. J. Med. Entomol. 61, 781-90.
Code/Software
All analyses were run in R v.4.0.4 and implemented the ENMTools package (Warren et al. 2021) and spThin (Aiello-Lammens et al. 2015). MaxEnt (v3.4.1) was used to generate species distribution models. In addition ENMeval package (v.2.0.4, Kass et al. 2021) was used to evaluate using a geographically structured 4 k-fold approach. Script for analyses and SDM generation are provided in the attached R script "ticks_ENMs.R"
Methods
Pathogen and host species distribution models
Species distribution models (SDM) for all D. occidentalis as well as infected D. occidentalis occurrences were generated using tick occurrence records and R. rickettsii californica infection status gathered from published studies and CDPH records (Paddock et al. 2018; Padgett et al. 2016). We georeferenced CDPH records based on zip code and county metadata associated with the tick samples by joining CDPH tick occurrence records with a 1999 US Census Bureau zip code gazetteer (Schuyler 2004). Mammal occurrence records were obtained through the VertNet database (http://vertnet.org) and observations that were not connected to an existing museum specimen were removed (California Academy of Sciences, UCLA-Dickey Bird and Mammal Collection, Field Museum of Natural History, Los Angeles County Museum, Museum of Vertebrate Zoology, Royal Ontario Museum, University of Kansas Biodiversity Institute, Yale Peabody Museum). For N. fuscipes, we used the occurrence records provided by a recent study which refined subspecies designations in museum records (Boria et al. 2020). We reduced sampling bias associated with collection data by spatially filtering occurrence points that were within a 5km radius of each other, due to the high spatial heterogeneity of California (Rissler et al, 2006), using ENMTools (Warren et al. 2021) and spThin (Aiello-Lammens et al. 2015) in R (v4.0.4).