DOI: 10.5061/dryad.7wm37pw1z
title: 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

description: 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.
description: <em>Pathogen and host species distribution
 models</em> Species distribution models (SDM) for
 all <em>D. occidentalis</em> as well as infected <em>D.
 occidentalis</em> occurrences were generated using tick occurrence
 records and <em>R. rickettsii californica</em> infection
 status gathered from published studies and CDPH records (Paddock et al.
 2018; Padgett et al<em>. </em>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 <em>N.
 fuscipes</em>, 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).
description: # 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](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](http://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](http://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](http://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](http://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](http://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](http://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](http://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](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](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 * [https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/Tick-Borne-Diseases.aspx#](https://www.cdph.ca.gov/Programs/CID/DCDC/Pages/Tick-Borne-Diseases.aspx#) 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](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](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"