Unique functional diversity during early Cenozoic mammal radiation of North America
Data files
Jun 04, 2024 version files 13.07 MB
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Datafile1_NAMammalTraits_Database.csv
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Datafile2_FunctionalCommunities_Final.csv
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Datafile3_1myr_TimeBin_Data.csv
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Datafile4_PrimaryReference_FDNA.csv
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Datafile5_LocalityDates.csv
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README.md
Abstract
Mammals influence nearly all aspects of energy flow and habitat structure in modern terrestrial ecosystems. However, anthropogenic effects likely have altered mammalian community structure, raising the question of how past perturbations have done so. We use functional diversity to describe how the structure of North American mammal communities changes over the past 66 Ma, an interval spanning the rebound radiation following the K/Pg and several subsequent environmental disruptions including the PETM, the expansion of grassland, and the onset of Pleistocene glaciation. For 264 fossil communities, we examine three aspects of ecological function: functional evenness, functional richness, and functional divergence. Shifts in functional diversity are significantly related to major ecological and environmental transitions. All three measures of functional diversity increase immediately following the extinction of the non-avian dinosaurs, suggesting that high degrees of ecological disturbance can lead to synchronous responses both locally and continentally. Otherwise, the components of functional diversity respond differently to environmental changes and are decoupled for the last ~56 million years.
README: North American Cenozoic Mammal Traits
This dataset includes information on fossil localities and mammal traits. The fossil localities and mammal occurrence data were collected from the Paleobiology Database (https://paleobiodb.org). Some locality dates were refined using the primary literature. The sources and information gathered for this process are included in the other datafile located on my Github (see link below) called "Locality_Date_Refinement".
The sources of each trait is listed as "Ref". Some may contain multiple sources. The "Other Sources" column was added when further sources were collected to infer traits of a species. The column "Alternative_Name" reflects another name the species may have been identified as in other databases where trait data was collected.
Description of the Data and file structure
CSV File Name: Datafile4_PrimaryReference_FDNA.csv
**Description of file: This file contains information downloaded from the Paleobiology Database providing information on the fossil collection used in this study. The database provides information about the original collectors, location and collection methodology. All cells filled with N/A represent information that is not available.
Variables:
- collection_no: The collection number as listed in the Paleobiology Database
- record_type: The type of record. All records included are 'col' or collection records.
- formation: The rock formation the collection is from.
- lng: longitude of the collection location
- lat: latitude of the collection location
- collection_name: the name of the collection identified in the primary literature
- collection_aka: Alternative name for the collection. Some collections do not have an alternative name are blank here.
- n_occs: the number of fossil occurrences that are from the collection in the Paleobiology Database
- early_interval: the earliest estimated time interval of the collection
- late_interval: the latest estimated time interval of the collection
- max_ma: maximum estimated age of the collection
- min_ma: minimum estimated age of the collection
- reference_no: the reference number as listed in the Paleobiology Database
- collection_methods: the field methodology used to collect specimens from the collection
- museum: the museum that the collection is stored in. Some museum information is unavailable.
- collection_coverage: The extent of faunal collection. Some information unavailable.
- collection_size: The number of specimens found in the collection.
- rock_censused: No data available
- collectors: The names of the people who were involved in the collection of the specimens
- collection_dates: The year that the collections were acquired. Some information unavailable
- collection_comments: Additional comments about the way the collection was acquired. Some information unavailable.
- taxonomy_comments: Additional comments about the specific locations that taxa were found or notes about significant findings. Some information unavailable.
- primary_reference: The primary published reference that first described this collection.
CSV File Name: Datafile5_LocalityDates.csv
**Description of file: A data frame of compiled information about the localities, formations, zones, units and members that allowed for a refinement of the locality dates. These refined age ranges are not meant to be able to target the exact age, but instead better estimate average than previously defined ranges provided by paleobio.org. Not all localities listed here were included in this study and many components. Any information that could be found to help refine the estimated age of a locality was added. However, the refined dates were typically found based on a single component (e.g., zone, fauna, member), all other components were left blank due to unavailable information. All cells filled with N/A represent information that is not available.
Variables:
- Formation: The rock formation
- Locality: The fossil locality name
- Unit: The unit of rock
- Member: The formation member
- Section: The section of the rock formation
- Group: The defined faunal group
- Magnetozones: The magnetozones of the defined area.
- Epoch/Age: The estimated epoch or age of the defined area
- Zone: The zone of the rock formation
- Subdivisions: The subdivisions of the rock formation that may combine multiple groups or faunas
- Sediment: The type of sediment that is character of the defined collection area
- Fauna: The fauna that represents the defined collection area
- Estimated_Date_Range: The refined estimated date range based on primary references
- Identified Interval Citation: Reference that provided an interval of time (e.g., epoch, age, etc.). For many localities no interval was identified and this was left blank.
- Interval Dating Citation (ma): Reference that provided refined dates for the locality
CSV File Name: Datafile3_1myr_TimeBin_Data.csv
**Description of file: **This datafile contains all calculated values used to evaluate functional diversity and abiotic and biotic factors in 1-million-year time bins. All cells filled with N/A represent information that is not available.
Variables:
- Ma: The 1-million-year time bin being represented
- Extinct_ml_rate: The extinction rate of the time bin
- Orig_ml_rate: The origination rate of the time bin
- observed: The observed number of species in the time bin
- synoptic: The estimated species richness of the time bin using the synoptic model
- chao2: The estimated species richness of the time bin using the chao2
- tripps: The estimated species richness of the time bin using the tripps model
- lognormal: The estimated species richness of the time bin using the lognormal model
- max_extrapolated: The maximum species richness estimated for the time bin
- do18: The averaged d018 values for the time bin
- do18_sd: The standard deviation of the d018 for the time bin
- Faunal_Prop.Archaic: The proportion of extinct orders within the time bin
- Fdiv_mean: The averaged functional divergence value calculated for the time bin
- Fric_mean: The averaged functional richness value calculated for the time bin
- Feve_mean: The averaged functional evenness value calculated for the time bin
- Faunal_Fric: The calculated functional richness for fauna in the time bin
- Faunal_Fdiv: The calculated functional divergence for fauna in the time bin
- Faunal_Feve: The calculated functional evenness for fauna in the time bin
- Epoch: The epoch that the time bin belongs to
- Local_PropArchaic_Mean: The average proportion of extinct orders for all localities within a time bin
- Feve_se: The standard deviation of the averaged functional evenness for a time bin
- Fric_se: The standard deviation of the averaged functional richness for a time bin
- Fdiv_se: The standard deviation of the averaged functional divergence for a time bin
CSV File Name: Datafile2_FunctionalCommunities_Final.csv
Description of file: This file contains calculations of each locality to evaluate changes in functional diversity over time.
Variables:
- Locality: The name of the locality
- Fric: Calculated functional richness
- Feve: Calculated functional evenness
- Fdiv: Calculated functional divergence
- lat: Latitude of the locality
- lng: Longitude of the locality
- Ma: The average estimated age of the locality
- dO18.st.dev: The standard deviation of the d018 values for the locality
- dO18: The d018 values averaged for the locality
- paleolat: The paleo-latitude
- paleolng: The paleo-longitude
- Species_Richness: The number of species in the locality
- Orders_Extinct: The number of orders extinct within the locality
- Prop.Archaic: The proportion of extinct orders in the locality
- Epoch: The epoch the locality is estimated to belong to.
- Date.Range: The difference in age between the earliest and latest date estimate.
- Mil_TimeBin: The 1-million-year time bin the locality belongs to.
- Fric_MassRemoved: Calculated functional richness value after the removal of body mass as a trait
- Fdiv_MassRemoved: Calculated functional divergence value after the removal of body mass as a trait
- Feve_MassRemoved: Calculated functional evenness value after the removal of body mass as a trait
CSV File Name: Datafile1_NAMammalTraits_Database.csv
**Description of file: **Database containing information about each mammal occurrence used in this study, including age, location, locality, collection, traits, and references. All cells filled with N/A represent information that is not available.
Variables:
- Collection_nu: The number of the collection as listed at paleobiodb.org
- Locality: Locality name as listed at paleobiodb.org
- Ma1:The latest estimated age of locality
- Ma: The average age of the locality based on the latest and earliest age estimates
- Ma2: The earliest estimated age of the locality
- Date Range: The range of time between the earliest and latest interval
- order: the taxonomic order of the species
- family: the taxonomic family of the species
- Species: The taxonomic species of name of the specimen
- Genus: The taxonomic genus of the specimen
- Name: The full species and genus name of the specimen
- order extinct: Whether or not the order is extinct (1=No, 0=Yes)
- LogMass g: The estimated body mass of the species in logged grams
- Diet: The diet of the species listed in the paleobiodb.org
- Locomotion: Morphological description of the locomotion style of the species based on references
- Life Habit: The life habit of a species based on where it primarily lives based on references
- Diet 2: If applicable, the secondary diet listed in paleobiodb.org
- Recode Diet: The final primary diet designated to the species for this study based on Diet 1 and Diet 2, as well as references
- Alternative_Name: The alternative name of the species
- Averaged: Indicates if the body mass was averaged at a higher taxonomic level than species. If blank, the average body mass was at the species level
- Mass.fill: Indicates how the average body mass was determined if not by species average
- Diet.Fill: Indicates how the species diet was determined if not by species
- Life.Habit.Fill: Indicates how the species life habit was determined if not by species
- Locomotion.Fill: Indicates how the species locomotion was determined if not by species
- Ref Diet: References used to define the diet of the species
- Ref Locomotion: References used to define the locomotion of the species
- Ref Life Habit: References used to define the life habit of the species
- Ref Recode Diet: References used to define the primary diet of the species
- Ref Mass: References used to define the average species body mass
- Other Sources: Any other references that provided additional information about the species traits that may have contributed to the decision to designate trait categories to a species.
- lng: longitudinal location
- lat: latitudinal location
- state: the state the occurrence was located
- paleolng: The paleo-latitute
- paleolat: The paleo-longitude
Sharing/access Information
Data and code for this study are available on my Github page https://github.com/Abshup22
Methods
Mammal occurrences were collected using the primary literature and paleobiology database. Mammal trait data was gathered from primary literature and various online databases including the paleobiology database and NOW database. All traits and occurrrences have a citation. All locality data information is available in a csv file. Dates were refined using the primary literature and all citations are provided in the document. I have the database attached as a csv file.