Capture and Morphometric Data from Ocelots around Laguna Atascosa National Wildlife Refuge from 2011-2021

This data package includes the original Excel spreadsheet, including the original terms (all rows and columns) as used by U.S. Fish and Wildlife Service as well as some additions that are required to meet the standards to be able to upload the data to Global Biodiversity Infrastructure Facility (GBIF.org) in the near future. This was done to improve useability of the dataset from ServCat while balancing the inclusion of terms that are standardized by Darwin Core Archive and the GBIF Internet Publishing Toolkit. Therefore, there may also be differences in the metadata found in the Service Catalog (ServCat) than in those of GBIF. In the future once the file is uploaded to GBIF, users experienced in the use of GBIF datasets may not have a use for the Excel file but instead find sufficient use for the GBIF (*.zip) data package. It may not appear identical to what is found at GBIF, as the upload and adjustments done through the process of uploading data to GBIF change how the data is organized and, in some cases, the original data is broken into associated files in the processes of GBIF. Making these data available to GBIF reaches a much broader audience of the global public than would uploads to ServCat alone. Data files from the GBIF process would be added to this reference in the future but the core data as presented in ServCat is not expected to change unless users find and point out errors. Darwin Core is a suite of standards terms, labels, and definitions that assist the scientific community in the sharing of biodiversity informatics. Terms in the dataset are mostly those in accordance with the Darwin Core (DwC) Standard (Darwin Core Task Group 2021) (http://rs.tdwg.org/dwc/terms/index.htm), but also include those of other standardized sources: the Phenotype And Trait Ontology (https://ontobee.org/ontology/PATO), the Vertebrate Trait Ontology (https://www.ebi.ac.uk/ols4/ontologies/vt/), and FuTRES Ontology of Vertebrate Traits (https://futres.org/how_it_works/). The Phenotype And Trait Ontology is a suite of standard term of phenotypic qualities (e.g., properties, attributes or characteristics). The Vertebrate Trait Ontology is a controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms. The FuTRES Ontology of Vertebrate Traits (FOVT) is a group of terms and definitions created by the FuTRES project to map measurable vertebrate traits for standardization across datasets regarding vertebrate morphology, physiology, and development. Users of the dataset should refer to those sources if more clarity is needed about a given field, or how it might relate to information from other databases. For any of those terms that we felt needed further explanation, or for those terms for which we could not find a common standard (the latter being identified below as “USFWS terms”), details are provided below. Terms The term occurrenceID includes the oranism name, the date of capture, and whether the ocelot was sedated, anesthetized for further monitoring (labelled as “Monitored”), or released without handling (labelled as “Released”. For the term organismName, “OF” signifies ocelot female, “OM” signifies ocelot male, and “OU” signifies ocelot of unknown sex. The three-digit code following the alpha-code was a unique number assigned to each individual ocelot and bobcat uniquely identified as part of the cat monitoring program at the Refuge; a system that was accurate and consistent since approximately 2007. The term lifeStage was a rough estimate of age (i.e., juvenile or adult) based in part on the study of ocelots in Texas, wherein the weight of ocelots appeared to be correlated with age in the kitten to subadult and even early adult stages (see chart below). Age estimated based on measured mass/weight 0 - 5 months = 3.4 kg or less 6 - 11 months = 3.4 - 6 kg 12 - 17 months = 5.1 - 6.6 kg 18 - 23 months = 6.2 - 7.2 kg Age estimates may have also been influenced based on teeth eruption, tooth wear (conditions recorded under the term “teethWear”) and any obvious adult reproductive characteristics. Age estimates may have also reflected staff knowledge based on photographs from remote cameras (and confidence in identification based on fur pattern from such animals). A frequently updated document was used by USFWS staff since ca. 2009 to track the history or “biography” of each ocelot known from the Refuge and this document also informed ageing estimates. The USFWS terms ageEstimateYearsMinimum, ageEstimateYearsMaximum, ageEstimateMonths were to assist the user in understanding the range of values USFWS staff placed on the individual at the time of capture and are relatively self-explanatory by name. In the field, during handling of a trapped ocelot, staff made notes on the estimated age in months for younger ocelots on occasion. To record these data for these younger ocelots, the term ageEstimateMonths was used. For all ocelots estimated to be of an age of 2 years or more, there was no value (i.e., “0”) given for the ageEstimateMonths field. For some individuals that were recorded with an estimate of, for example, “4.5 to 5.5 years old”, we found no record for such precision, and their age was rounded up to the next year, e.g., 5 to 6 years old, in the case of the example given. Following this example, the field for ageEstimateYearsMinimum would have been 5, and the field for ageEstimateYearsMaximum would have been 6. For any such individual that either age was not recorded later, we simply increased the minimum and maximums through time. For any individual (e.g., OM301) not caught enough to provide more information and was quite heavy at first capture and staff recorded age as, for example, “2+” [years], these individuals were assigned (in this example) a minimum age of 3, and a maximum of 5, intending to skip a year for the maximum as a notification to data users that the ocelot may indeed be much older than the age estimate. In the case of individuals that staff estimated to be for example 15 months old, ageEstimateYearsMinimum was recorded as 1 (year), ageEstimateYearsMaximum was recorded as 1 (year), and ageEstimateMonths was recorded as 3 (months). In the singular case of an individual (i.e., OM283) that staff estimated as 9-12 months, ageEstimateYearsMinimum was recorded as 0 (year), ageEstimateYearsMaximum was recorded as 1 (year), and ageEstimateMonths was recorded as 9 (months); that estimates not be confused to suggest that staff believed the individual was estimated to be 21 months old. If age was left unrecorded in the digital database that was being curated for public release, we used age estimates from previous capture data and used the dynamic “biographies” documents USFWS staff maintained until 2021 to corroborate the age estimate assignment in this dataset. In this dataset all ocelots estimated as 2 years old were classified as adults due to their weight. But from the standpoint of their physiological development, their independence from their dam, or as having an independent territory, etc, those items were not assessed in the assignment of an age estimate. Therefore, users should use the data for these relatively young ocelots with precaution if ranking them as adults, possibly considering other evidence such as measured weight, etc, to assess whether they consider the lifeStage value is accurate and appropriate for subsequent analyses. The USFWS term estBirthdate was based upon expert knowledge of individual ocelots and in some cases was recorded on the field datasheet and subsequent dataset. To provide a standard date format, we added/assigned the first day of the month from their birthdate estimate. In summary, measurements are presented here in kg for mass (weight) of the ocelot, and mm for canine length, and all other measures in cm. The term mass is based on the definition of the Phenotype And Trait Ontology source and is measured in kg in this dataset. Mass is preferred to the term weight by this standard. The term neckCircumference_cm was recorded in values of cm in this dataset. The VTO defined this term as “Any measurable or observable characteristic related to the shape, structure, color or pattern of the portion of the body that extends from the head to the pectoral girdle, encompassing the cervical vertebral column”. The neck was measured using a flexible tape wrapped around the longest axis of the neck. The term headCircumference_cm was recorded in values of cm in this dataset. It is a term defined by the Vertebrate Trait Ontology as “the distance around the widest part of the portion of the body containing the brain and organs of sight, hearing, taste, and smell”. The head was measured using a flexible tape wrapped around the longest axis of the cranium as described. The term bodyLength comes from FuTRES Ontology of Vertebrate Traits (FOVT) source and was recorded in values of cm in this dataset. The measurement was intended to include the length of the head, neck, torso, and tail. The FOVT defines it as the “length of a body that includes the tail”, which includes from the point of the nose to the longest point of the tail. The term bodyLength might have been more appropriately labelled in this dataset as a longer descriptor “body length with tail”. The term tailLength_cm was recorded in values of cm in this dataset. The VTO defines this term as the “distance from point to point along the longest axis of the appendage at the caudal end of the vertebral column”. It appears that in some cases staff were not including the tail measurement as part of the total bodyLength value. Users might want to consider adding the recorded tailLength_cm value to the bodyLength value if the bodyLength seems considerably shorter (e.g., compared to previous measures, or in comparison to ocelots of similar mass) such that an error in recording is suspected. In many cases we believe the (total) bodyLength value did not include the tail (e.g., OM283 on 2016 0412). Overall, users should use caution in making broad interpretations about differences in measurements for the same individual across years. The term rightHindFootLength_cm was a term from the FuTRES Ontology of Vertebrate Traits source and this measure was recorded in values of cm in this dataset. In our application the right hindfoot was the standard appendage measured. The right hindfoot was measured from the tip of the nail to the furthest end of the calcaneum. The term rightHindFootLength_cm is synonymous with “pes length with nail” by some other sources for standard terms. The USFWS terms leftCanine_mm and rightCanineLength_mm were recorded in values of mm in this dataset. This term was not found explicitly as a standard term among the available ontology standards although we reference the definition from VTO as “Any measurable or observable characteristic related to the shape, structure, color or pattern of the bone-like structures embedded in the jaw and used for mastication”. The top canines were measured from the gumline to the tip of the canine and recorded in mm, or in cm and converted to mm, for this dataset. The USFWS term teethWear was not found as a standard term among the available ontology standards. Rating of teeth wear was not necessarily standardized across all staff and years; staff rated the wear and condition of the teeth visually and on a 4-tiered score: none, minimal, moderate, severe. The classification of “heavy” was used by staff and changed in this dataset to be more qualitative as opposed to appearing as if it were a measure of mass; the value of “heavy” was replaced with the value “severe”. There were also remarks made about the teeth such as chipped teeth, apparent tartar or build-up on teeth, and missing teeth on some occasions, but we felt these values may have been inconsistently assessed or recorded and did not include them. For any measures that were not recorded the value entered was “NR”.