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'''A Dataset of Amphibian Species in U.S. National Parks''' is a research article that describes a new synthesis of amphibian occurrence data in the U.S. National Park Service (NPS) system.
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'''A Dataset of Amphibian Species in U.S. National Parks''' is a research article published in Nature on the 4th January 2024 that describes a new synthesis of amphibian occurrence data in the U.S. National Park Service (NPS) system.
== Summary ==
* '''Data collection and validation''' - the authors updated and verified the amphibian data from NPSpecies, a multi-taxa database of species observations in national park units, by cross-checking with various sources and regional experts.
* '''Data collection and validation''' - the authors updated and verified the amphibian data from NPSpecies, a multi-taxa database of species observations in national park units, by cross-checking with various sources and regional experts.
* '''Data records and availability''' - the verified dataset contains 2,742 records of 230 amphibian species across 292 NPS units, and includes updated taxonomy, conservation status, references, and notes. The dataset is available at NPS DataStore with a DOI link.
* '''Data records and availability''' - the verified dataset contains 2,742 records of 230 amphibian species across 292 NPS units, and includes updated taxonomy, conservation status, references, and notes. The dataset is available at NPS DataStore with a DOI link.
* '''Technical validation and code availability''' - the verified dataset underwent considerable technical validation, such as removing unverifiable records, normalizing taxonomy, assigning conservation status, and comparing with published range maps. No custom code was used to generate or process the data.
* '''Technical validation and code availability''' - the verified dataset underwent considerable technical validation, such as removing unverifiable records, normalizing taxonomy, assigning conservation status, and comparing with published range maps. No custom code was used to generate or process the data.


== Abstract ==
<pdf>File:A Dataset of Amphibian Species in U.S. National Parks (research).pdf</pdf>
National parks and other protected areas are important for preserving landscapes and biodiversity worldwide. An essential component of the mission of the United States (U.S.) National Park Service (NPS) requires understanding and maintaining accurate inventories of species on protected lands. We describe a new, national-scale synthesis of amphibian species occurrence in the NPS system. Many park units have a list of amphibian species observed within their borders compiled from various sources and available publicly through the NPSpecies platform. However, many of the observations in NPSpecies remain unverified and the lists are often outdated. We updated the amphibian dataset for each park unit by collating old and new park-level records and had them verified by regional experts. The new dataset contains occurrence records for 292 of the 424 NPS units and includes updated taxonomy, international and state conservation rankings, hyperlinks to a supporting reference for each record, specific notes, and related fields which can be used to better understand and manage amphibian biodiversity within a single park or group of parks.
 
== Background & Summary ==
With habitat loss as a major driver decreasing biodiversity, protected areas are increasingly essential to conservation<sup>1,2,3,4</sup>. The U.S. National Park Service (NPS) manages a wide variety of lands protected from development, overuse, overharvesting, and other potentially impactful activities. Although most NPS units were established to protect historical, cultural, or geologically unique features, these protected park units can also be important for conservation of species such as amphibians5,6. The unusual geologic and natural features that characterize some national parks and protected areas likely contribute to the presence of endemic species or distinct populations7,8. To better understand how NPS lands contribute to amphibian diversity in the U.S. (Table 1), we updated a dataset of amphibian species occurrence in each park unit that had records in NPSpecies.
{| class="wikitable"
|+Table 1
!UCN status
!No. of species in USA
!No. of species on NPS land
!Percent of species documented on NPS land
|-
|Least Concern
|186
|158
|85.0
|-
|Near Threatened
|36
|17
|47.2
|-
|Vulnerable
|33
|10
|30.3
|-
|Endangered
|20
|6
|30.0
|-
|Critically Endangered
|7
|0
|0.0
|-
|Extinct in the Wild
|1
|0
|0.0
|-
|Extinct
|2
|0
|0.0
|-
|Data Deficient
|69
|39
|56.6
|-
|Total
|354
|230
|65.0
|}
As a starting point for our updated dataset, we began with the amphibian data available from the NPSpecies platform, an NPS multi-taxa database of species observations in national park units9. The associated metadata in the original NPSpecies database included a 4-letter park code to denote where the species observation occurred, the species taxonomy (filled in at each park’s discretion without following uniform taxonomy), “GRank” and “SRank” based on NatureServe status (over a third of the records had no data in this column), a nativeness column, as well as other fields such as “ozone” which is important for other species monitored by the NPS (such as ozone sensitive plants) but is extraneous for this dataset. Information about the specific date of observations in NPSpecies is limited.
 
As of 01 March 2021, NPSpecies had 4,198 records of amphibian species across all park units. Although NPSpecies is internally validated, over 1,000 of the records were still listed as unconfirmed or unverified. We used available nomenclature in the Integrated Taxonomic Information System (ITIS) to provide a common taxonomy for consistency and comparability10,11. We also cleaned the NPSpecies list by removing 836 unverifiable park-level species occurrences and adding 115 new occurrences, changing occurrence status or taxonomy on over 1,000 records, and had regional subject matter experts verify the updated records (Fig. 1). As an example of changing occurrence status and cleaning the data, Death Valley National Park had 71 amphibian species listed in NPSpecies, but only 10 species were verified as Present, Adjacent, or even Possibly Present. A list of all associated data and definitions (such as what Present, Adjacent or Possible mean) for each record are in Table 212. The 115 new records were added opportunistically when references or regional subject matter experts that verified an original record (see below) had additional information about species or park records not yet documented in parks13. No additional data sources (e.g., HerpMapper or iNaturalist) were used for adding new species during this initial dataset revision.
{| class="wikitable"
|+Table 2
!Column Heading
!Description
|-
|Park_Code
|The 4-letter acronym to identify the specific park unit
|-
|Park_Name
|Full name of the national park unit
|-
|IM_Network
|The 4-letter acronym for the associated NPS Inventory and Monitoring Network
|-
|CASC_Region
|The 2-letter acronym for the associated Climate Adaptation Science Center region
|-
|State
|The US state that the specific park lies within (for the centroid of the park)
|-
|TSN
|Taxonomic Serial Number, unique identifier for each amphibian species in accordance with ITIS
|-
|Order
|Taxonomic order of amphibians for the species (Anura or Caudata)
|-
|Family
|Taxonomic family of the species
|-
|Scientific_Name
|Scientific name for the amphibian (''Genus'' + ''specific epithet'')
|-
|Common_Names
|Common names used for the species
|-
|Verified_Date
|The date when the observation was verified (ISO standard format of YYYY-MM-DD)
|-
| rowspan="6" |Park_OccurrenceStatus
|Verified status in park—Present, Possible, Adjacent, Historic, No; updated from NPSpecies “Occurrence” field also included
|-
|Present = the species is present within this park unit
|-
|Possible = the species is possibly found on this park unit but has not been confirmed
|-
|Adjacent = the species has been found on land near but not within this park unit (often within ~50 km)
|-
|Historic = this species has been observed in this park in the past (before the year 2000), but is unlikely to be found now
|-
|No = this species has not been observed in this park based on our research
|-
|Notes
|Notes included during the verification process (includes both primary and secondary verification)
|-
|Verified_Source
|Link or note regarding reference material (report, primary literature, etc.)
|-
|Park_Synonyms
|Alternative scientific name (outdated, ITIS invalid, subspecies, or park preferred name)
|-
|NPSpecies_Occurrence
|Present, Probably Present, Unconfirmed, Not in Park (designation in 2021 version of NPSpecies)
|-
|NPSpecies_OccTag
|More information regarding occurrence (Historical; False Report) from the 2021 version of NPSpecies
|-
|Abundance
|NPS ranking akin to IUCN Status—Abundant, Common, Occasional, Uncommon, Rare, Unknown
|-
|Nativeness
|Whether species is native, non-native, or unknown
|-
|GRank
|Global Conservation Status Rank (data from www.natureserve.org)
|-
|SRank
|Sub-national rank for the species (field indicates the state by two-letter code, followed by the status)
|-
|IUCNRank
|The conservation status of the species as defined on the International Union for Conservation of Nature (IUCN) Red List
|}
Many of these columns can also be found in the NPSpecies User Guide12.
 
Overall, the updated dataset accounts for approximately 70% of the units managed by the NPS (Fig. 2), and only includes those parks originally present within the 2021 version of NPSpecies dataset. Based on species lists from AmphibiaWeb, International Union for Conservation of Nature (IUCN), the USGS National Amphibian Atlas (as of 08 May 2023)14,15, approximately 65% of the amphibian species documented in the U.S. were found in NPS managed areas (230 of 354; Table 1). A few species (mostly ''Eleutherodactylus'' and ''Desmognathus'') not listed in any of the above sources, but which have verified occurrences from published sources were included in the dataset13. As with any national-scale project with ongoing efforts, this list is not exhaustive and some species that might actually or possibly exist on or near NPS lands may not be included. Similarly, the dynamic status and uncertainty around taxonomic classification for some species, such as many frogs in the family Hylidae and salamanders in the ''Desmognathus'' and ''Plethodon'' genera, likely contributes a small amount of error or ephemerality to the new dataset. Also, there are additional resources for amphibian data in the U.S. (e.g., iNaturalist, GBIF, HerpMapper) that may provide updates to the NPSpecies data archive16,17. Future efforts may focus on the integration of more complete occurrence records from all NPS units with managed lands and other sources.
 
== Methods ==
 
=== Data collection ===
The final dataset was built from initial data downloaded from NPSpecies9, which consisted of 4,198 amphibian records as of 01 March 2021. We performed an initial validation which consisted of spending approximately 1 hour per park unit cross-checking the NPSpecies data against primary literature, reports, theses, range maps19, and verified iNaturalist observations. Each record was given a hyperlink to a reference as well as any relevant notes about the record or citation. After initial verification, the dataset was taxonomically normalized in accordance with ITIS11. All subspecies designations and non-standard nomenclature was retained in the “ParkSynonyms” field.
 
Records which lacked specificity (only family- or genus-level information provided) were deleted, as well as any obviously false or unverifiable observations (e.g., where a species was recorded well outside of its published range). Upon taxonomic normalization and initial dataset cleaning, we contacted regional subject matter experts to perform a final verification and comment on observations specific to their region. Finally, each record was assigned a conservation status. The global rank (GRank) and state rank (SRank) were based on NatureServe data20, as well as a the previously mentioned status based on the IUCN Red List15. To aid in management, each dataset entry was also given a field to denote its assignment to one of the 32 NPS Inventory and Monitoring Networks21.
 
== Data Records ==
The verified dataset maintains a similar format to that represented in NPSpecies, comprised of a single CSV file. Each row of the spreadsheet indicates a unique park-level species occurrence record, while each column heading provides information about that record. Information about each column is given in Table 2. The dataset is available at NPS DataStore (<nowiki>https://doi.org/10.57830/2301647)18</nowiki>.
 
== Technical Validation ==
The verified dataset underwent considerable technical validation. Initial verification was performed by the first two authors of this manuscript, spending approximately 1 hour per park obtaining references for each record within the dataset. Next, the following steps were used to improve dataset quality and comparability: (1) records with “absent” occurrence data and no verifiable references to the contrary were removed, as absent data can be misleading and are rarely reported in occurrence datasets; (2) records with no species-level information were removed; (3) record taxonomy was normalized to ITIS valid species names as of 2022; (4) any missing information for each original record was added for completeness (i.e., some original records were missing values in fields such as nativeness, GRank, SRank, and common names); and (5) species occurrence records were cross-checked with published range maps19. Range maps often overestimate species distributions. Any park with species records outside the known range map was scrutinized to either reclassify the species to accurately reflect the range or remove the record entirely. For example, most NPS park units in the western United States still list ''Ambystoma tigrinum'' as the tiger salamander species present even though the western tiger salamander (''A. mavortium'') was described as a distinct species in 199622.
 
As a final technical verification, regional subject matter experts were asked to provide comments and verify each record relevant to their geography. As a final check, the verified dataset was compared back to the original NPSpecies records, noting all discrepancies and changes (Fig. 3). For example, for the 2,665 species occurrence records in NPSpecies “Present” category, 2,436 were also classified as ''Present'' within the verified, updated dataset. However, for the remaining ''Present'' records in the updated dataset, 88 records were originally classified as ''Possibly Present'', 32 records were originally classified as ''Not in the Park'', 104 records were originally unclassified (either unconfirmed or not given a designation), and 82 new records were added. Also, instead of the original intermediate classification of ''Probably Present'', which indicates some significant likelihood that is difficult to represent by occurrence data, we use the more neutral term ''Possible''. All these updates and technical validations align with best practices employed in other large occurrence datasets23,24,25.
 
== Code availability ==
No custom code was used to generate or process the data described in this manuscript.
 
== References ==
 
# Halstead, B. J. ''et al''. Looking ahead, guided by the past: The role of U.S. national parks in amphibian research and conservation. ''Ecol. Indic.'' 136, 108631 (2022).  Article Google Scholar
# Lawrence, D. J. ''et al''. National parks as protected areas for U.S. freshwater fish diversity. ''Conserv. Lett.'' 4, 364–371 (2011).  Article Google Scholar
# Rodhouse, T. J., Philippi, T. E., Monahan, W. B. & Castle, K. T. A macroecological perspective on strategic bat conservation in the U.S. National Park Service. ''Ecosphere'' 7, e01576 (2016).  Article Google Scholar
# Wu, J. X., Wilsey, C. B., Taylor, L. & Schuurman, G. W. Projected avifaunal responses to climate change across the U.S. National Park System. ''PLoS ONE'' 13, e0190557 (2018).  Article PubMed PubMed Central Google Scholar
# U.S. Congress. ''National Park Service Organic Act of 1916 (16 U.S.C §1 1916)''. (1916).
# National Park Service. Management Policies: The Guide to Managing the National Park System. <nowiki>https://www.nps.gov/subjects/policy/upload/MP_2006.pdf</nowiki>. (2006).
# Ray, A. ''et al''. Do Newts at Crater Lake Represent a Distinctly Evolving Population of Rough-skinned Newts? ''Herpetol. Conserv. Biol.'' 17, 521–538 (2022).  Google Scholar
# Grant, E. H. C., Brand, A. B., De Wekker, S. F. J., Lee, T. R. & Wofford, J. E. B. Evidence that climate sets the lower elevation range limit in a high-elevation endemic salamander. ''Ecol. Evol.'' 8, 7553–7562 (2018).  Article PubMed PubMed Central Google Scholar
# National Park Service. NPSpecies, version 01 March 2021. The National Park Service biodiversity database. <nowiki>https://irma.nps.gov/npspecies/</nowiki> (2021).
# Frost, D. Amphibians of the World, an Online Reference, version 6.1. ''American Museum of Natural History''. <nowiki>https://amphibiansoftheworld.amnh.org/</nowiki> (2022).
# ITIS. Integrated Taxonomic Information System. ''ITIS'' <nowiki>https://doi.org/10.5066/F7KH0KBK(2022)</nowiki>.
# National Park Service. NPSpecies User Guide - Integrated Resource Management Applications Portal <nowiki>https://irma.nps.gov/content/npspecies/Help/docs/NPSpecies_User_Guide.pdf</nowiki> (2019).
# Pyron, R. A. & Beamer, D. A. Systematic revision of the Spotted and Northern Dusky Salamanders (Plethodontidae: ''Desmognathus conanti'' and ''D. fuscus''), with six new species from the eastern United States. ''Zootaxa'' 5311, 451–504 (2023).  Article PubMed Google Scholar
# AmphibiaWeb. University of California, Berkeley, CA, USA. <nowiki>https://amphibiaweb.org/(2023)</nowiki>.
# International Union for the Conservation of Nature and Natural Resources. The IUCN Red List of Threatened Species, version 20-2. <nowiki>http://www.iucnredlist.org</nowiki> (2022).
# GBIF.org Occurrence download. ''Global Biodiversity Information Facility''<nowiki>https://doi.org/10.15468/dl.fnzpdw</nowiki> (2022).
# HerpMapper. HerpMapper - A Global Herp Atlas and Data Hub. Iowa, USA. <nowiki>http://www.herpmapper.org</nowiki> (2023).
# LaFrance, BJ., & Ray, AM. A Dataset of Amphibian Species in U.S. National Parks, version 1.3, ''National Park Service.'', <nowiki>https://doi.org/10.57830/2301647</nowiki> (2023).
# U.S. Geological Survey (USGS). U.S. Geological Survey - Gap Analysis Project Species Range Maps CONUS_2001, ''USGS'', <nowiki>https://doi.org/10.5066/F7Q81B3R</nowiki> (2018).
# NatureServe. NatureServe Network Biodiversity Location Data accessed through NatureServe Explorer. <nowiki>https://explorer.natureserve.org/</nowiki> (2022).
# Fancy, S. G., Gross, J. E. & Carter, S. L. Monitoring the condition of natural resources in US national parks. ''Environ. Monit. Assess.'' 151, 161–174 (2009).  Article CAS PubMed Google Scholar
# Shaffer, H. B. & McKnight, M. L. The polytypic species revisited: genetic differentiation and molecular phylogenetics of the tiger salamander ''Ambystoma tigrinum'' (amphibia: caudata) complex. ''Evolution'' 50, 417–433 (1996).  Article CAS PubMed Google Scholar
# Petersen, T. K., Speed, J. D. M., Grøtan, V. & Austrheim, G. Species data for understanding biodiversity dynamics: The what, where and when of species occurrence data collection. ''Ecol. Solut. and Evid.'' 2, e12048 (2021).  Article Google Scholar
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Download references
 
== Acknowledgements ==
The authors acknowledge the Great Lakes Network, Greater Yellowstone Network, Sonoran Desert Network, and Southern Plains Network of the NPS Inventory and Monitoring Division, and the USGS Amphibian Research and Monitoring Initiative (ARMI) for providing funding for this project. We thank R. Brodman for help verifying species accounts. We thank Kristin Legg and Dusty Perkins for comments on previous versions of this manuscript. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. This is contribution 883 of the USGS Amphibian Research and Monitoring Initiative.
 
== Author information ==


=== Authors and Affiliations ===
== See also ==


# Northern Rockies Conservation Cooperative, Jackson, WY, 83001, USA  Benjamin J. LaFrance
* [[:Category: Amphibian (research)]]
# National Park Service—Greater Yellowstone Network, Bozeman, MT, 59715, USA Benjamin J. LaFrance
* [[:Category: USA (research)]]
# National Park Service—Southern Plains Network, Pecos, NM, 87552, USA  Andrew M. Ray
# U.S. Geological Survey—Western Ecological Research Center, San Diego, CA, 92101, USA  Robert N. Fisher
# U.S. Geological Survey—Eastern Ecological Research Center (Patuxent Wildlife Research Center), Turners Falls, MA, 01376, USA  Evan H. Campbell Grant & Charles Shafer
# Office of Research, Economic Development and Engagement, East Carolina University, Greenville, NC, 27858, USA  David A. Beamer
# U.S. Geological Survey—Upper Midwest Environmental Sciences Center, La Crosse, WI, 54603, USA  Stephen F. Spear
# Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, GA, 30144, USA  Todd W. Pierson
# Department of Biology, Appalachian State University, Boone, NC, 28608, USA  Jon M. Davenport
# Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA  Matthew L. Niemiller
# Department of Biological Sciences, The George Washington University, Washington, DC, 20052, USA  R. Alexander Pyron
# Department of Vertebrate Zoology, National Museum of Natural History Smithsonian Institution, Washington, DC, 20560, USA  R. Alexander Pyron
# U.S. Geological Survey—Wetland and Aquatic Research Center, Lafayette, LA, 70506, USA  Brad M. Glorioso
# U.S. Geological Survey—Wetland and Aquatic Research Center, Gainesville, FL, 32653, USA  William J. Barichivich
# U.S. Geological Survey—Western Ecological Research Center, Dixon, CA, 95620, USA  Brian J. Halstead
# Arkansas Herpetological Atlas, Bella Vista, AR, 72715, USA  Kory G. Roberts
# U.S. Geological Survey—Northern Rocky Mountain Science Center; Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA  Blake R. Hossack


=== Contributions ===
== External links ==
B.J.L., A.M.R. and B.R.H. conceptualized and designed the study. B.J.L. and A.M.R. performed the initial verification of all records. All other authors performed secondary expert verification and are listed in order of the number of records verified. B.J.L., A.M.R. and B.R.H. wrote the manuscript, and the manuscript was edited and revised by all authors. All authors approved the manuscript for submission.


=== Corresponding author ===
* https://doi.org/10.1038/s41597-023-02836-2 DOI
Correspondence to Andrew M. Ray.
* [https://irma.nps.gov/DataStore/Reference/Profile/2301647 A Dataset of Amphibian Species in U.S. National Parks, Version 1.3] DPS Datastore
[[Category:Amphibian (research)]]
[[Category:USA (research)]]

Latest revision as of 16:33, 9 January 2024

A Dataset of Amphibian Species in U.S. National Parks (research)

A Dataset of Amphibian Species in U.S. National Parks is a research article published in Nature on the 4th January 2024 that describes a new synthesis of amphibian occurrence data in the U.S. National Park Service (NPS) system.

Summary

  • Data collection and validation - the authors updated and verified the amphibian data from NPSpecies, a multi-taxa database of species observations in national park units, by cross-checking with various sources and regional experts.
  • Data records and availability - the verified dataset contains 2,742 records of 230 amphibian species across 292 NPS units, and includes updated taxonomy, conservation status, references, and notes. The dataset is available at NPS DataStore with a DOI link.
  • Technical validation and code availability - the verified dataset underwent considerable technical validation, such as removing unverifiable records, normalizing taxonomy, assigning conservation status, and comparing with published range maps. No custom code was used to generate or process the data.

See also

External links

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