Dataset DOI: 10.5061/dryad.gf1vhhn3v

Description of the data and file structure

Howard_GSA_continuous Excel file contains measurements and presence/absence states of each studied species from literature and museum collections at the American Museum of Natural History, the National Museum of Natural History, and the Field Museum.

1. Name: Name of species measured
2. ub/lb: upper boundary/lower boundary. Highest and lowest measurement for each character.
3. deg_involution: degree of involution, or how much of the umbilicus is covered by the outer whorls of the adult shell.
4. whorl_shape: height of adult whorl divided by width of adult whorl.
5. shell_inflation: whorl width at greatest point divided by shell diameter.
6. whorl_ex_rate: height of last whorl divided by height of second-to-last whorl on adult shell.
7. aperture_overlap: Height of aperture overlapping inner whorl divided by total aperture height.
8. max_aperture_width: Length from top of aperture to widest point of aperture divided by total aperture height.
9. ventral_width: Width of adult venter divided by shell diameter.
10. sinuousity_index: Complexity of suture pattern.
11. ex_saddle_height: External saddle height divided by lateral saddle height, measured from base to top of each projection.
12. u_saddle_height: First U saddle height divided by lateral saddle height, measured from base to top of each projection.
13. ex_saddle_h/w: External saddle height divided by external saddle width.
14. lat_saddle_h/w: Lateral saddle height divided by lateral saddle width.
15. rib_h/w: Adult rib height divided by rib width.
16. rib_rate: Rib width, measured from crest to crest, divided by shell diameter.

Howard_GSA_final(2) (1) Nexus file contains character states for species within the ammonoid family Acanthoceratidae based on raw measurements found in the Excel file. Character states include both continuous and discrete characters, including overall shape and size of species and presence/absence of certain characters for each species studied.

1. Adult IVL tubercle presence: Presence or absence of tubercles on the inner area of the shell, near the adult venter.

2. Adult IVL tubercle type: Appearance of tubercles on the inner area of the shell, near the adult venter.

3. Adult most prominent tubercle: Position of the most prominent tubercle on adult whorls.

4. Adult OVL tubercle presence: Presence or absence of tubercles on OVL position on adult whorl, between venter and umbilicus.

5. Adult OVL tubercle type: Appearance of tubercles on OVL position on adult whorl, between venter and umbilicus.

6. Adult umbilical tubercle presence: Presence or absence of tubercles on umbilical position of adult whorl.

7. Adult umbilical tubercle type: Appearance of tubercles on umbilical position of adult whorl.

8. Adult ventral tubercle presence: Presence or absence of tubercles on ventral position of adult whorl.

9. Adult ventral tubercle type: Appearance of tubercles on ventral position of adult whorl.

10. Adult whorls section shape: Overall shape of adult whorl.

11. Aperture overlap: Height of aperture overlapping inner whorl divided by total aperture height.

12. Constriction of lateral saddle: Absence or presence of a constricted appearance of lateral saddle on adult whorl.

13. Degree of Involution: Umbilical diameter divided by overall diameter.

14. Direction of ribs umbilical to ventral: Direction ribs bend, when examined from an umbilical to ventral position.

15. Division of external saddle: Number of projections within the external saddle portion of adult suture.

16. Division of first U saddle: Number of projections within the first U saddle portion of adult suture.

17. Division of lateral lobe: Number of projections within the lateral lobe portion of adult suture.

18. Division of lateral saddle: Number of projections within the lateral saddle portion of adult suture.

19. External lobe depth: External lobe depth divided by lateral saddle height, measured from base to top of each projection.

20. External lobe depth vs. lateral lobe depth: Lobe with the deepest projection, between external and lateral lobes.

21. External saddle height: External saddle height divided by lateral saddle height, measured from base to top of each projection.

22. External saddle height over width: External saddle height divided by external saddle width.

23. First U saddle deepest element: Location of longest projection in first U saddle position.

24. first U saddle height: First U saddle height divided by lateral saddle height, measured from base to top of each projection.

25. First U saddle position relative to lateral saddle position: Direction suture pattern drifts from lateral saddle position to U saddle position.

26. First U saddle shape: Overall shape of first U saddle.

27. Juvenile IVL tubercle presence: Presence or absence of tubercles on inner area of shell, near the juvenile venter.

28. Juvenile IVL tubercle type: Appearance of tubercles on inner area of shell, near the juvenile venter.

29. Juvenile most prominent tubercle: Position of most prominent tubercle on juvenile whorls.

30. Juvenile OVL tubercle presence: Presence or absence of tubercles on OVL position on juvenile whorl, between venter and umbilicus.

31. Juvenile OVL tubercle type: Appearance of tubercles on OVL position on juvenile whorl, between venter and umbilicus.

32. Juvenile umbilical tubercle presence: Presence or absence of tubercles on umbilical position on juvenile whorl.

33. Juvenile umbilical tubercle type: Appearance of tubercles on umbilical position of juvenile whorl.

34. Juvenile ventral tubercle presence: Presence or absence of tubercles on ventral position of juvenile whorl.

35. Juvenile ventral tubercle type: Appearance of tubercles on ventral position of juvenile whorl.

36. Keel: Presence or absence of keel on adult whorl.

37. Lateral saddle deepest element: Location of longest projection in lateral saddle position.

38. Lateral saddle height over width: Lateral saddle height divided by lateral saddle width.

39. Lateral saddle shape: Overall shape of lateral saddle.

40. Position of maximum aperture width: Length from top of aperture to widest point of aperture divided by total aperture height.

41. Presence of secondary ribs: Presence or absence of smaller ribbing between larger, primary ribs.

42. Rib height over width: Rib height measured from trough to crest divided by rib width, measured from crest to crest.

43. Rib rate: Rib width, measured from crest to crest divided by shell diameter.

44. Shell inflation: Whorl width at greatest point divided by shell diameter.

45. Sinuousity Index: Complexity of suture pattern.

46. Skew of lateral saddle: Direction lateral saddle tilts when examined from venter to umbilicus.

47. Symmetry in first U saddle: Absence or presence of symmetry within the first U saddle.

48. Symmetry in lateral lobe: Absence or presence of symmetry within lateral lobe.

49. Symmetry in lateral saddle: Absence or presence of symmetry within lateral saddle.

50. Ventral migration of tubercles: Absence or presence of tubercles migrating towards venter as juvenile shell transfers to adult shell.

51. ventral width: Width of adult venter divided by shell diameter.

52. Whorl expansion rate: Height of final whorl divided by height of previous whorl.

53. Whorl shape: Final whorl width divided by final whorl height.

    Paleobiology_Database (PBDB) file in the Common_R_Source_Files folder contains downloaded information on ammonoid family Acanthoceratidae from the PaleoBiology Database, downloaded on 11/20/2025 by the authors.

Files and variables

File: Disparity_Paper_Code_Dryad.zip

Description: Folder includes basic R scripts as well as source files and data for executing the analyses described in this paper. 

File: Simulations_Random_Differences.r

Description: R script for producing a set of simulated phylogenetic trees based on real compatibility of measured characters. Simulations available include "Random", where branches in the phylogenetic tree are placed randomly, and "Differences", where branches in the phylogenetic tree are placed based on differences between groupings or hypothetical genera.

File: Inter_vs_Intra_Taxon_Disparity_4.r

Description: R script for comparing disparity of inter- and intrageneric species based on measured characters. 

Following files contain functions used in main code, along with data not specific to this study.

File: Chronos.r

Description: Functions to deal with absolute time and time scales.

File: Compatibility.r

Description: Routines to determine compatibility of a set of characters, used in Simulations_Random_Differences.r

File: Data_Downloading_v4.r

Description: Routines used to download data from the Paleobiology Database (PBDB), and to curate the data so that R can use it.

File: Disparity.r

Description: Routines for different types of disparity analyses.

File: General_Plot_Templates.r

Description: Routines to produce various plots, including stratigraphic figures.

File: General_Plot_Templates_for_Class.r

Description: More routines to produce various plots.

File: Gradstein_2020_Augmented.rdata

Description: Data file containing the Gradstein et al. 2020 geologic time scale.

$time_scale: set up of time scale for Gradstein

1. record_no: record number 
2. interval: time interval name
3. interval_alt: alternative time interval name
4. interval_sr: old time interval name
5. chronostratrigraphic_rank: rank of chronostratigraphy 
6. scale: scale of time rank
7. ma_lb: lower boundary of time in millions of years ago
8. ma_up: upper boundary of time in millions of years ago
9. ma_lb_2012: lower boundary of time in millions of years ago from 2012
10. ma_ub_2012: upper boundary of time in millions of years ago from 2012
11. color: color
12. st: stage
13. basal_biozone_zone_no: zone number of basal biozone
14. basal_biozone: name of basal biozone
15. basal_biozone_scale: scale of time rank of basal biozone
16. basal_zone_modifier: modifier for basal biozone
17. terminal_biozone_no: biozone number at terminal point
18. terminal_biozone: biozone at terminal point
19. terminal_biozone_scale: scale of time rank of biozone at terminal point
20. terminal_zone_modifier: modifier for biozone at terminal point
21. created: date created
22. modified: date modified

$zones: set up of zones for Gradstein

1. zone_type: type of zone
2. zone: name of zone
3. zone_sr: former name of zone
4. regional_scale: what region the zone is in
5. ma_lb: lower boundary of time in millions of years ago
6. ma_up: upper boundary of time in millions of years ago
7. ma_lb_2012: lower boundary of time in millions of years ago from 2012
8. ma_up_2012: upper boundary of time in millions of years ago from 2012
9. interval_lb: lower boundary interval
10. interval_up: upper boundary interval
11. record_no: record number
12. zone_no_sr: old version of record number
13. created: date created
14. modified: date modified
15. zone_species: species name of zone
16. zone_species_sr: old species name of zone
17. non_taxon_zone: zone without biozone taxa
18. non_taxon_zone_label: label of zone without biozone taxa
19. non_taxon_zone_sr: old zone without biozone taxa
20. non_taxon_zone_label_sr: old label of zone without biozone taxa
21. genus_species_combo: full Latin binomial of biozone taxa
22. subgenus_species_combo: full Latin binomial plus subspecies name of applicable biozone taxa
23. zone_epithet: name of zone
24. zone_epithet_sr: old name of zone
25. abbreviated_zone: abbreviated name of zone

File: Historical_Diversity_Metrics.r

Description: Routines to estimate different aspects of historical diversity patterns.

File: Nexus_File_Routines.r

Description: Routines to import and curate data from nexus files saved by phylogenetic program Mesquite.

File: Occurrence_Data_Routines.r

Description: Routines to clean and curate occurrence data drawn from the PBDB.

File: paleo_tree_extras.r

Description: Routines used to develop a phylogenetic tree in R based on imported nexus files.

File: Paleobiology_Database.rdata

$pbdb_finds: dataframe with information about the occurrences from the Paleobiology Database

1. occurrence_no: occurrence number
2. record_type: record type
3. reid_no: reid number, not used
4. flags: flags yes/no
5. collection_no: collection number
6. identified_name: identified name
7. identified_rank: identified rank
8. identified_no: identified number
9. difference: if there have been any recombinations or renames
10. accepted_name: accepted name
11. accepted_rank: rank of accepted name
12. accepted_no: accepted number
13. early_interval: first interval
14. late_interval: last interval
15. max_ma: maximum date in millions of years
16. min_ma: minimum date in millions of years
17. ref_author: author referenced
18. ref_pubyr: year reference was published
19. reference_no: reference number
20. phylum: phylum
21. phylum_no: phylum  number
22. class: class
23. class_no: class number
24. order: order
25. order_no: order number
26. family: family
27. family_no: family number
28. genus: genus
29. genus_no: genus number
30. subgenus_no: subgenus number
31. occurrence_comments: any comments about the documented occurrence
32. authorizer: name of authorizer of occurrence
33. enterer: name of enterer of occurrence
34. modifier: name of modifier of occurrence
35. updater: name of updater of occurrence
36. abund_value: abundance value
37. abund_units: abundance unit
38. created: date and time created
39. modified: date and time modified
40. updated: date and time updated
41. accepted_name_orig: original accepted name

$pbdb_sites: dataframe with information about the site of the occurrences from the PBDB

1. collection_no: collection number
2. record_type: record type
3. _label: record label
4. _status: record status
5. permissions: permissions, if needed
6. authorization: type of authorization granted
7. lng: longitude
8. collection_name: name of collection
9. collection_aka: nickname of collection, if needed
10. n_occs: number of occurrences
11. early_interval: early interval of site
12. late_interval: late interval of site
13. max_ma: maximum age of site in millions of years
14. min_ma: minimum age of site in millions of years
15. ref_author: reference author
16. ref_pubyr: year reference was published
17. reference_no: reference number
18. cc: site country
19. state: site state
20. county: site county
21. latlng_basis: how author set latitude and longitude
22. latlng_precision: how precise the latitude and longitude is
23. altitude_value: value of altitude
24. altitude_unit: unit of altitude
25. geogscale: scale of geography of site
26. geogcomments: comments on geography of site
27. paleomodel: model of paleosite
28. geoplate: geoplate
29. paleolng: longitutde of paleosite
30. paleolat: latitude of paleosite
31. formation: formation
32. paleoage: age of site
33. geological_group: geological group
34. member: member of formation
35. stratscale: scale of stratigraphy
36. zone: zone of site
37. zone_type: type of zone
38. localsection: location of section
39. localbed: location of bed
40. localbedunit: location of bed unit
41. localorder: location of order
42. regionalsection: region of section
43. regionalbed: region of bed
44. regionalbedunit: region of bed unit
45. regionalorder: region of order
46. stratcomments: comments on stratigraphy
47. time_bins: time bin of site
48. time_contain: site contains what time bins
49. time_major: majority of time bin of site
50. time_buffer: boundary time of site
51. time_overlap: any overlapping time bin of site
52. lithdescript: description of lithology
53. lithology1: first lithology
54. lithadj1: adjusted lithology of lithology1
55. lithification1: presence or absence of lithification of lithology1
56. minor_lithology1: minor lithologies of lithology1
57. fossilsfrom1: fossils found in lithology1
58. lithology2: second lithology
59. lithadj2: adjusted lithology of lithology2
60. lithification2: presence or absence of lithification of lithology2
61. minor_lithology2: minor lithologies of lithology2
62. fossilsfrom2: fossils found in lithology2
63. environment: paleoenvironment of site
64. tectonic_setting: tectonic setting
65. geology_comments: comments on geology of site
66. collection_type: collection type
67. collection_methods: methods of collection
68. museum: where collection is curated
69. collection_coverage: amount of coverage of collection
70. collection_size: collection size
71. rock_censused: rocks that were censused
72. collectors: name of collector(s)
73. collection_dates: date of collection
74. collection_comments: comments on collection
75. taxonomy_comments: comments on taxonomy of fossils
76. research_group: research group
77. primary_reference: primary reference
78. authorizer_no: authorizer number
79. enterer_no: enterer number
80. modifier_no: modifier number
81. updater_no: updater number
82. authorizer: name of authorizer
83. enterer: name of enterer
84. modifier: name of modifier
85. editor: name of editor
86. created: date and time created
87. modified: date and time modified
88. lat: latitude
89. updated: date and time updated
90. collection_subset: collection subset
91. direct_ma: date in millions of years ago
92. direct_ma_error: date in millions of years ago with error
93. direct_ma_method: method used to edit date in millions of years ago
94. formation_alt: alternative name for formation
95. member_alt: alternative name for member
96. geological_group_alt: alternative name for geological group
97. interval_lb: lower boundary of interval
98. interval_ub: upper boundary of interval

$pbdb_taxonomy: dataframe with information about the taxonomy of the collected material

1. orig_no: original number
2. taxon_no: taxon number
3. record_type: type of record
4. flags: presence or absence of flags
5. taxon_rank: rank of taxon
6. taxon_name: name of taxon
7. taxon_attr: taxon name attributed to author
8. common_name: common name
9. difference: any potential synonyms
10. accepted_no: accepted number
11. accepted_rank: accepted rank
12. accepted_name: accepted name
13. parent_no: higher clade number
14. parent_name: higher clade name
15. immpar_no: number of clade opposite collection clade
16. immpar_name: name of clade opposite collection clade
17. ref_author: reference author
18. ref_pubyr: year reference was published
19. reference_no: reference number
20. is_extant: is exctinct or extant
21. n_occs: number of occurrences
22. firstapp_max_ma: maximum date of first appearance in millions of years ago
23. firstapp_min_ma: minimum date of first appearance in millions of years ago
24. lastapp_max_ma: maximum date of last appearance in millions of years ago
25. lastapp_min_ma: minimum date of last appearance in millions of years ago
26. early_interval: name of early interval
27. late_interval: name of late interval
28. taxon_size: size of taxon
29. extant_size: size of extant members of a taxon
30. phylum: name of phylum
31. phylum_no: phylum number
32. class: name of class
33. class_no: class number
34. order: name of order
35. order_no: order number
36. family: name of family
37. family_no: family number
38. genus: name of genus
39. genus_no: genus number
40. subgenus_no: subgenus number
41. type_taxon: name of type taxon
42. n_orders: number of orders
43. n_families: number of families
44. n_genera: number of genera
45. n_species: number of species
46. taxon_environment: natural environment of taxon
47. environment_basis: how conclusion for taxon_environment was formed
48. motility: how mobile taxon was
49. motility_basis: how conclusion for motility was formed
50. life_habit: life history of the taxon
51. life_habit_basis: how conclusion for life_habit was formed
52. vision: visual ability of taxon
53. vision_basis: how conclusion for vision was formed
54. diet: what the taxon consumed
55. diet_basis: how conclusion for diet was formed
56. reproduction: how taxon reproduced
57. reproduction_basis: how conclusion for reproduction was formed
58. ontogeny: how the taxon developed from juvenile to adult
59. ontogeny_basis: how conclusion for ontogeny was formed
60. ecospace_comments: comments on ecospace of taxon
61. composition: what the taxon was composed of
62. architecture: architecture of the taxon
63. thickness: thickness of occurrence
64. reinforcement: reinforcement of occurrence
65. taphonomy_basis: how conclusion for taphonomy was formed
66. lft: left string of numbers attached to occurrence
67. rgt: right string of numbers attached to occurrence
68. image_no: image number of taxon
69. primary_reference: primary reference for occurrence
70. authorizer_no: authorizer number
71. enterer_no: enterer number
72. modifier_no: modifier number
73. updater_no: updater number
74. authorizer: authorizer name
75. enterer: enterer name
76. modifier: modifier name
77. updater: updater name
78. created: date and time created
79. modified: date and time modified
80. updated: date and time updated

$pbdb_opinions: dataframe with information about the opinions written about each occurrence

1. opinion_no: opinion number
2. record_type: record type
3. opinion_type: opinion type
4. taxon_rank: taxon rank
5. taxon_name: taxon name
6. orig_no: original number
7. child_name: name of lower taxonomic rank
8. child_spelling_no: number of lower taxonomic rank
9. status: belongs to or is a part of next column
10. parent_name: name of higher taxonomic rank
11. parent_no: number of higher taxonomic rank
12. parent_spelling_no: number of higher taxonomic rank spelling
13. spelling_reason: note if misspelling
14. basis: what is opinion based on
15. author: author of opinion
16. pubyr: publication year of opinion
17. ref_author: author of reference
18. ref_pubyr: year of reference
19. reference_no: reference number
20. primary_reference: primary reference for opinion
21. authorizer_no: authorizer number
22. enterer_no: enterer number
23. modifer_no: modifier number
24. updater_no: updater number
25. authorizer: name of authorizer
26. enterer: name of enterer
27. modifier: name of modifier
28. updater: name of updater
29. created: date and time created
30. modified: date and time modified
31. updated: date and time updated

$pbdb_sites_refined: same as $pbdb_sites

$pbdb_finds_oldid: same as $pbdb_finds, with old names

$extended_paleogeography: dataframe with extended information about paleogeography

1. collection_no: collection number
2. paleomodel1: name of first model placing paleogeography
3. paleolat1: paleolatitude from paleomodel1
4. paleolng1: paleolongitude from paleomodel1
5. paleomodel2: name of second model placing paleogeography
6. paleolat2: paleolatitude from paleomodel2
7. paleolng2: paleolongitude from paleomodel2
8. paleomodel3: name of third model placing paleogeography
9. paleolat3: paleolatitude from paleomodel3
10. paleolng3: paleolongitude from paleomodel3
11. paleomodel4: name of fourth model placing paleogeography
12. paleolat4: paleolatitude from paleomodel4
13. paleolng4: paleolongitude from paleomodel4
14. paleomodel5: name of fifth model placing paleogeography
15. paleolat5: paleolatitude from paleomodel5
16. paleolng5: paleolongitude from paleomodel5
17. paleomodel6: name of sixth model placing paleogeography
18. paleolat6: paleolatitude from paleomodel6
19. paleolng6: paleolongitude from paleomodel6
20. modified: date modified

$time_scale: dataframe connecting information about time scale to occurrences

1. record_no: record number
2. interval: interval
3. interval_alt: alternative interval
4. interval_sr: old version of interval
5. chronostratigraphic_rank: chronostratigraphic rank
6. scale: scale of time bin
7. ma_lb: lower boundary of time bin in millions of years ago
8. ma_ub: upper boundary of time bin in millions of years ago
9. ma_lb_2012: lower boundary of time bin set in 2012 in millions of years ago
10. ma_ub_2012: upper boundary of time bin set in 2012 in millions of years ago
11. color: color
12. st: stage
13. basal_biozone_zone_no: basal biozone zone number
14. basal_biozone: basal biozone
15. basal_biozone_scale: basal biozone scale
16. basal_zone_modifier: modifier to basal zone, if used
17. terminal_biozone_zone_no: terminal biozone zone number
18. terminal_biozone: terminal biozone
19. terminal_biozone_scale: terminal biozone scale
20. terminal_zone_modifier: modifier to terminal zone, if used
21. created: date created
22. modified: date modified

$pbdb_rocks: dataframe of formations connected to occurrences

1. rock_no_orig: original rock number
2. rock_no: rock number
3. rock_no_sr: old rock number
4. formation_no: formation number
5. group: group
6. formation: formation
7. member: member
8. full_name: full name of rock formation
9. formation_clean_basic: cleaned formation name
10. formation_clean_no_rock: rock formation cleaned number
11. formation_clean_no_rock_formal: formal formation cleaned number
12. member_clean_basic: cleaned member name
13. member_clean_no_rock: rock member cleaned number
14. member_clean_no_rock_formal: formal member cleaned number
15. group_clean_no_rock_formal: formal group cleaned number
16. group_clean_no_rock: rock group cleaned number
17. group_clean_basic: cleaned group name
18. rock_unit_clean_basic: cleaned rock unit name
19. rock_unit_clean_no_rock: cleaned rock unit number
20. rock_unit_clean_no_rock_formal: formal rock unit cleaned number

$single_binners: dataframe of occurrences in only one time bin

1. periods: time period of time bin
2. single_binner_number: number of each occurrence in a single time bin

Description: Ammonoid data downloaded from the PBDB on 10/3/24

File: paleophylogeny_routines.r

Description: Like paleo_tree_extras.r, Routines used to develop a phylogenetic tree in R based on imported nexus files.

File: phylogeny_simulations.r

Description: Routines to simulate a phylogenetic tree based on compatibility of a set of characters.

File: RevBayes_Setup.r

Description: Routines to prepare the data to be imported into RevBayes for further phylogenetic analysis.

File: Sepkoski_Genus_Compendium.rdata

Description: R data file containing an up-to-date list of genera included in the PBDB.

1. Genus_No: genus number
2. Phylum: phylum
3. Class: class
4. Order: order
5. Genus: genus
6. pbdb_taxon_no: taxon number in PBDB
7. status: synonym or misspelling of other taxon
8. Genus_23: genus as of 2023
9. pbdb_accepted_no: accepted number in PBDB
10. FA: first appearance
11. LA: last appearance
12. Ref_1: first reference
13. Ref_2: second reference
14. Ref_3: third reference
15. Ref_4: fourth reference
16. Ref_5: fifth reference
17. Synonym: synonym, if any
18. Phylum_98: phylum
19. Class_98: class
20. Order_98: order

File: Wagner_kluges.r

Description: A set of routines used to prepare data for the main code's analysis, written by one of the authors (Wagner).

File: Wagner_Stats_and_Probability_101.r

Description: A set of routines written by one of the authors (Wagner) for basic statistics and probability analysis.

Code/software

RStudio is required to run the code files included. R code version 4.4.1 was used for the final version of these files. 

Most packages used for these files are included in the folder "Common_Source_R_Files," but the package "readxl" is also needed to load in the data files.