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Skeletons of Terrestrial Cetaceans and the Relationship of Whales to Artiodactyls Supplementary Information


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Skeletons of Terrestrial Cetaceans and the Relationship of Whales to Artiodactyls

Supplementary Information

J. G. M. Thewissen*, E. M. Williams*, L.J. Roe†, and S.T. Hussain‡

*Anatomy Department, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272, U.S.A.

†Department of Geosciences, University of Arizona, Tucson, AZ 85721, U.S.A.

‡Department of Anatomy, Howard University, College of Medicine, Washington D.C. 20059, U.S.A.
Correspondence Author: J. G. M. Thewissen (thewisse@neoucom.edu)
Table of Contents
Part I. Classification and Character List

Part II. Data Matrix

Part III. Consensus Tree of Analysis

Part IV. Most Parsimonious Trees

Part V. Apomorphy List for Cetartiodactyla and Artiodactyla Nodes (ACCTRAN and DELTRAN optimization)

Part VI. Bootstrap Analysis



PART I. Classification and Character List

The following taxa are included in our analysis: Arctocyon, Hyopsodus, Phenacodus, Meniscotherium, Andrewsarchus, Eoconodon, Hapalodectes, Dissacus, Ankalagon, Sinonyx, Harpagolestes, Mesonyx, Pachyaena, Synoplotherium, Pakicetus, Ambulocetus, Diacodexis pakistanensis, Diacodexis secans, Archeotherium, Elomeryx (based on Elomeryx and Bothriodon), Hippopotamus, Hexaprotodon, Sus, Agriochoerus, Poebrotherium, Tragulus, Haplobunodontidae (based on Anthracobunodon and Haplobunodon), Cebochoeridae (based on Gervachoerus and Cebochoerus), and Raoellidae (based on Indohyus, Kunmunella, and Khirtharia). We follow the classification provided below.


Condylarths

Family Arctocyonidae



Arctocyon

Family Hyopsodontidae



Hyopsodus

Order PHENACODONTA

Family Phenacodontidae

Phenacodus

Meniscotherium

Grandorder PARAXONIA

Order MESONYCHIA (probably paraphyletic)

Family Andrewsarchidae (possibly paraphyletic)



Andrewsarchus

Eoconodon


Family Hapalodectidae

Hapalodectes

Family Mesonychidae



Dissacus

Ankalagon

Sinonyx

Pachyaena

Mesonyx

Harpagolestes

Synoplotherium

Mirorder CETARTIODACTYLA

Order CETACEA

Family Pakicetidae



Pakicetus

Nalacetus

Ichthyolestes

Family Ambulocetidae



Ambulocetus

Order ARTIODACTYLA

Family Dichobunidae (paraphyletic)

Diacodexis (paraphyletic genus)

D. pakistanensis

D. secans

Family Entelodontidae



Archaeotherium

Family Anthracotheriidae



Elomeryx

Bothriodon

Family Hippopotamidae



Hippopotamus

Hexaprotodon

Family Suidae



Sus

Family Raoellidae



Indohyus

Khirtharia

Kunmunella

Family Cebochoeridae



Gervachoerus

Cebochoerus


Family Haplobunodontidae

Anthracobunodon

Haplobunodon

Family Agriochoeridae



Agriochoerus

Family Camelidae



Poebrotherium

Family Tragulidae



Tragulus
The characters listed below are mainly based on the following sources: Geisler and Luo (1998); Gentry and Hooker (1988); Luckett and Hong (1998); Luo and Gingerich (1999); Novacek (1986); O’Leary and Rose (1995); O’Leary (1998); O’Leary and Geisler (1999); Theodor (1996); Thewissen (1994); Thewissen and Madar (1999); and Zhou et al. (1995). References listed with each character are the primary source for our interpretation of that character, not necessarily the first use of it.


  1. P1/, single-rooted (0), two-rooted (1) (modified from O’Leary, 1998).

  2. P3/, three-rooted (0), two-rooted (1) (Zhou et al., 1995).

  3. P4/, protocone present (0) or absent (1) (Thewissen, 1994).

  4. P4/, paracone similar in height to M1/ paracone (0), or greater than twice that height (1) (Thewissen, 1994).

  5. P4/, metacone absent (0) or present (1) (Thewissen and Domning, 1992).

  6. M1/, parastyle absent (0) or present (1) (modified from O’Leary, 1998).

  7. M2/, metacone similar in height to paracone (0), or smaller (1) (Zhou et al., 1995).

  8. M2/, trigon basin large (0), or small (1) (Thewissen, 1994).

  9. M2/, paraconule present (0), or absent (1) (O’Leary, 1998; O’Leary and Geisler, 1999).

  10. M2/, metaconule absent (0), present and similar in size to paraconule (1), or hypertrophied, approaching the size of the protocone (2), ordered (modified from O’Leary and Geisler, 1999 following Gentry and Hooker, 1988).

  11. M2/, hypocone absent (0), present and small (1), present and similar in size to protocone (2), ordered (modified from O’Leary and Geisler, 1999).

  12. M2/, centrocrista straight (0), or labially deflected (1). This is a measure of selenodonty.

  13. M2/, mesostyle absent (0), or present (1) (Thewissen and Domning, 1992).

  14. M3/, similar or slightly larger than M2/ (0), smaller than M2/ (1) or absent (2), ordered (modified after O’Leary and Geisler, 1999).

  15. I/1-3, small, spatulate (0), large tusks (1) (O’Leary and Geisler, 1999).

  16. C/1, approximately twice as large as incisors (0), or similar in size (1) (O’Leary and Geisler, 1999).

  17. C/1, cross-section oval (0), or triangular (1) (Gentry and Hooker, 1988)

  18. P/1, present (0), or absent (1) (Zhou et al., 1995).

  19. P/3, metaconid absent (0), or present (1) (Thewissen and Domning, 1992).

  20. P/4, metaconid absent (0), or present (1) (Thewissen and Domning, 1992).

  21. P/4, talonid with cusp (0), or without cusp (1).

  22. M/2, paraconid present (0), or absent (1) (O’Leary and Geisler, 1999).

  23. M/2, paracristid (and/or paraconid) directed lingually (0), or anterior (1) (O’Leary, 1998; O’Leary and Geisler, 1999).

  24. M/2, metaconid present (0), or absent (1) (Zhou et al., 1995).

  25. M/2, trigonid similar in height to talonid (0), at least twice as high (1) (modified from O’Leary, 1998).

  26. M/2, hypoconulid present (0), or absent (1) (O’Leary and Geisler, 1999).

  27. M/2, entoconid present (0), or absent (1) (modified after O’Leary and Geisler, 1999).

  28. M/2 metaconid and entoconid cuspate (0) or elongate, merged into an antero-posterior extending crest (1). This is a measure of selenodonty.

  29. M/2, reentrant grooves on anterior side of tooth absent (0) or present (1) (Thewissen, 1994; modified after O’Leary and Geisler, 1999).

  30. M/3, hypoconulid, large, forming a third lobe (0), small (1), or absent (2), ordered (Thewissen, 1994; O’Leary and Geisler, 1999).

  31. Elongate shearing facets on molars, absent (0), present, extending below the gum line (1) (O’Leary and Geisler, 1999).

  32. D/4, paracristid connects protoconid and paraconid (0), additional cusp present on paracristid (Gentry and Hooker, 1988; Luckett and Hong, 1998).

  33. Mandible, ventral angular process absent (0), or present (1) (Gentry and Hooker, 1988; O’Leary and Geisler, 1999).

  34. Premaxilla, incisors arranged in arc (0), or antero-posterior row (1) (Thewissen, 1994).

  35. Maxilla, embrasure pits absent (0) or present (1) (Thewissen, 1994).

  36. Naso-lacrimal contact on face, absent (0) or present (1).

  37. Lacrimal shape on face, similar in dorso-ventral height and antero-posterior width (0), or large exposure with length much more than height (1) (Thewissen, 1994).

  38. Lacrimal tubercle, absent (0) or present (1) (Novacek, 1986).

  39. Orbit, contact between frontal and maxilla absent (0) or present (1) (Thewissen and Domning, 1992).

  40. Postorbital process of frontal, absent (0), present (1) (modified after O’Leary and Geisler, 1999).

  41. Supraorbital foramen absent (0) or present (1).

  42. Intertemporal region wide (0) or narrow, less than half the width of the palate (1).

  43. Nasopharyngeal duct lacks a bony ventral side (0), or ossified ventral border (1) (modified after Thewissen, 1994).

  44. Ectopterygoid process, present (0) or absent (1) (Thewissen and Domning, 1992).

  45. Round foramen absent (0), or present (1) (Thewissen and Domning, 1992).

  46. Alisphenoid canal absent (0) or present (1) (Thewissen and Domning, 1992).

  47. Oval foramen in alisphenoid (0) or on suture between alisphenoid and petrosal (1) (modified from O’Leary and Geisler, 1999).

  48. Glenoid fossa without (0) or with (1) preglenoid tubercle (Thewissen, 1994)

  49. Postglenoid process smooth posteriorly (0) or indented by external auditory meatus (1).

  50. Postglenoid foramen present (0), or absent (1) (Novacek, 1986; modified after Geisler and Luo 1998).

  51. Glenoid fossa medially bordered by a crest or elevated out or plane of basicranium (0), medially continuous with middle ear cavity or tympanic (1).

  52. Tegmen tympani shape, uninflated (0), or inflated (1) (Cifelli, 1982; modified after Geisler and Luo, 1998).

  53. Petrosal, anterior process absent (0), or present, extending far anterior to pars cochlearis (1) (modified after Geisler and Luo, 1998).

  54. Tensor tympani, fossa shallow and elongate (0), or circular (1), or circular with deep anterior groove (2) (modified after Geisler and Luo, 1998).

  55. Internal carotid artery, no separate foramen for its entrance into the braincase anterior to the pars cochlearis (0), or foramen present (1) (Geisler and Luo, 1998).

  56. Internal carotid artery, sulcus on promontorium present (0) or absent (1) (Cifelli, 1982; Thewissen and Domning, 1992).

  57. Stapedial artery, sulcus on promontorium present (0), or absent (1) (Cifelli, 1982; Thewissen and Domning, 1992).

  58. Foramen for superior ramus of stapedial artery present (0) or absent (1) (modified from Novacek, 1986).

  59. Suture between pars cochlearis of petrosal and basisphenoid/basioccipital present (0) or absent (1) (Thewissen and Domning, 1992).

  60. Ectotympanic, ring-shaped (0), bulla-shaped (1) (Geisler and Luo,1998).

  61. Ectotympanic thin-walled (0) or with thick-walled involucrum (1) (modified from Thewissen, 1994).

  62. Furrow on caudal tympanic for tympanohyal absent (0) or present (1) (modified after Geisler and Luo, 1998).

  63. Sigmoid process absent (0) or present (1) (Thewissen, 1994).

  64. Ectotympanic does not (0) or does form part of tubular external auditory meatus (1) (modified after Geisler and Luo, 1998).

  65. Hypoglossal foramen close to occipital condyle (0) or closer to jugular foramen (1) (Thewissen, 1994).

  66. Condyloid foramen, absent (0), separate from hypoglossal foramen (1) (Geisler and Luo, 1998)

  67. Subarcuate fossa, present (0) or absent (1) (Novacek, 1986).

  68. Mastoid exposed on posterior side of braincase between squamosal and occipital (0), or no posterior exposure (1) (Thewissen and Domning, 1992).

  69. Mastoid foramen, present piercing mastoid (0), or absent (1) (see MacPhee, 1994).

  70. Posttemporal canal, present on petro-squamous suture in posterior view (0), or absent (1) (Wible, 1990; MacPhee, 1994).

  71. Revolute zygapophyses of lumbar vertebrae, absent (0), or present (1).

  72. Number of sacral vertebrae, less than four (0), four (1), or more than four (2), ordered (Thewissen and Domning, 1992; Gingerich et al., 1995)

  73. Scapula, acromion overhangs glenoid (0), or does not (1) (modified after O’Leary and Rose, 1995).

  74. Humeral head, rounded (0), or medio-laterally narrow (1).

  75. Deltoid tuberosity present (0), or absent (1) (Theodor, 1996).

  76. Entepicondyle of humerus wide (0), or narrow (1) (modified after O’Leary and Rose, 1995).

  77. Entepicondylar foramen present (0), or absent (1) (Thewissen and Domning, 1992).

  78. Olecranon process short, up to 10% of ulnar length (0), or long (1) (derived from O’Leary and Rose, 1995)

  79. Radius, single fossa for distal humerus (0), two fossae (1), or three fossae (2), ordered (modified from Geisler and Luo, 1998). This character can also be scored on the basis of the humerus.

  80. Radius, single distal fossa for carpals (0), or two separate fossae (1) (derived from O’Leary and Rose, 1995).

  81. Radius and ulna distally unfused (0), or fused (1) (Theodor, 1996).

  82. Centrale, present (0) or absent (1) (Thewissen, 1994).

  83. Manus mesaxonic (0), or paraxonic (1) (O’Leary and Geisler, 1999).

  84. Distal phalanges, strongly concave palmar/plantar border (0); or flat border (1) (derived from MacLeod and Rose, 1993).

  85. Distal phalanges in dorsal view, narrow transversely (0), broad transversely (1) (modified after MacLeod and Rose, 1993).

  86. Femur, greater trochanter height, less than head (0), or even/higher (1) (modified after O’Leary and Rose, 1995).

  87. Femur, third trochanter present (0), or absent (1) (modified after O’Leary and Rose, 1995).

  88. Femur, patellar groove wide (0), or narrow (1) (O’Leary and Geisler, 1999).

  89. Fibulo-calcaneal joint absent (0), or present (1) (Thewissen and Madar, 1999).

  90. Astragalar canal present (0), or absent (1) (modified after Shoshani, 1986; Thewissen and Domning, 1992).

  91. Astragalus, (proximal) trochlea flat or weakly grooved (0) or deeply excavated (1) (Schaeffer, 1947; O’Leary and Rose, 1995).

  92. Astragalar head mediolaterally convex (0), or flat/concave (1) (Thewissen and Madar, 1999).

  93. Astragalar head dorso-plantarly mildly convex (0), or strongly convex (1) (as described by Thewissen and Madar, 1999).

  94. Astragalo-navicular joint lacks defined plane of rotation (0), rotates in dorso-plantar plane (1), or in oblique plane (2) (modified after Thewissen and Madar, 1999).

  95. Astragalo-cuboid contact absent (0), or present (1) (Thewissen and Madar, 1999).

  96. Sustentacular facet oval and medial (0), or rectangular and wide (1) (rescored after Thewissen and Madar,1999).

  97. Distal calcaneal facet of astragalus indistinct from sustentacular facet (0), or distinct (1); Thewissen and Madar, 1999).

  98. Ectal facet concave and facing plantar (0), or flat and facing lateral (1) (Thewissen and Madar, 1999).

  99. Calcaneo-cuboid joint oval and facing distal (0), or elongate and oblique (1) (Thewissen and Madar, 1999).

  100. Cuboid and navicular unfused (0), or fused (1) (Webb and Taylor, 1980).

  101. Ectocuneiform and mesocuneiform unfused (0), or fused (1).

  102. Pes, mesaxonic (0), paraxonic (1) (Thewissen, 1994).

  103. Metatarsal I, unreduced (0), somewhat reduced, less than 50 % of length of MT III (1), or absent/tiny splint (2), ordered (O’Leary and Geisler, 1999).

  104. Metatarsals II, unreduced (0), or less than 50% of length of MT III (1), or absent/tiny splint (2), ordered (Theodor,1996; O’Leary and Geisler, 1999).

  105. Metatarsals III and IV, unfused (0), or fused (1) (Theodor, 1996; modified after O’Leary and Geisler, 1999).



PART II. Data Matrix

#NEXUS
begin data;

dimensions ntax=29 nchar=105;

format symbols= " 0 1 2" missing=- gaps=-;



matrix

Arctocyon 0000000010 1100000000 0000010001 0000000100 0001100100 0000-0000- ----000000 1-00000000 10-0100010 0000100000 0-000


Hyopsodus 0000000001 2000000011 0000000001 00000001-0 0000010000 0101-0000- ----000000 -100000011 0001000-10 0000001000 000—
Phenacodus 0000100001 2011000011 0100000001 00000-0100 000-010000 0-00-11101 -0000--010 01-0000011 0101110100 0000100000 00100
Meniscotherium 00001-0001 2011000001 0100010001 00000001-0 0000110100 0100-00--- ----000010 0100000011 0101110110 00-0001000 00100
Andrewsarchus 000-00-110 0000---0-- 0-----00-0 0--00----- -0---1-10- ---------- ---------- ---------- ---------- ---------- -----
Eoconodon 0000000101 1100000000 0000110000 0-0-0--1-0 -----100-- ---1011-1- -------0-0 ----000-1- 0-------11 01--1----- -----
Hapalodectes 000-11-110 1-00--00-0 0010111012 0-001-001- 1001110000 0-00100-0- ----01-010 ------0--- ---------- ---------- -----
Dissacus 0000111110 0100000000 0010111002 0-0-0----- --1--101-1 0101-000-- ----0100-0 ---1100-11 ---11--1-0 0112101000 -----
Ankalagon -00011111- 0100000000 -0101-1002 0--------- ---------- ---------- ---------- -----10-1- ---11--0-0 01-------0 -----
Sinonyx 0000011110 0100000000 0010111002 0-0000010- 010111-111 0--1-0--01 001-11-0-0 ---------- ---------- ---------- -----
Pachyaena 0-0011-110 0100000000 0011111002 00000--1-- ---------- ---------- --11---010 1000010111 0011110-00 0112100000 01-00
Mesonyx 0-00011111 0200--0000 0011111002 00000----- 000-11010- 0101000011 0011--10-0 0010010111 0011110100 011210---0 -1200
Synoplotherium --0--11110 01000000-0 -01-111002 0-000001-0 000-11010- 0--------1 -01100-000 1000-10111 0011110101 01121----0 01200
Harpagolestes 0100111110 020000-1-- 00111-1002 0--0---1-- -101-10100 0--------1 001100-0-0 ---001011- ------0--0 01-------- -----
Pakicetus -111011110 0000000000 1001111010 10011100-1 1111000111 11-10--101 1110110001 110-011111 0-11110111 111111111- 1-200
Ambulocetus -111011110 0000----00 1101111012 1-011--0-1 -11100-11- -------001 111011-0-- 01---11101 01111101-- 1--------- 11200
D_pakistanensis 1000010001 0000000000 1000000000 0-01000011 1001000000 1---00--10 0111110001 11-0011111 0110010111 1111111110 01200
D_secans -000010001 1000----00 1000000000 010------- -001000000 11-100000- ----11-111 -110111-21 0--1011111 1111111110 -1200
Archaeotherium 01010-0001 1000000000 1000000000 0100000001 1--100000- -001-011-1 0011--1111 -01--11121 --110001-1 11----1110 11220
Elomeryx 1100010002 0011000011 0000000100 011000-101 1-01000010 -101011101 0011001101 --10011121 01111--11- 1111111110 11100
Hippopotamus 0100010011 1000001100 0000000010 0110010011 1-0100100- -10-011111 0011--11-- -21--11111 -111110111 1111111110 01200
Hexaprotodon 0000000011 1000001011 0000000000 0110000010 1-010-100- -1-----111 00-1--11-- -21--11121 -111111111 0111111110 01-00
Sus 1100110001 1001001101 0000000000 0110000100 1001001000 1001011111 0111101111 1110-11121 0111111111 1111111110 01200
Agriochoerus 1000110012 0011--0101 1000010100 01000001-0 1-0100000- -00-000-11 0111--0001 1-10001021 01-1001111 1111111110 11200
Poebrotherium 1100010012 1011000001 1000010110 0100000011 1-0100000- -001-11-01 0111--0001 -01--11021 --11011111 1111111110 11220
Tragulus -100-00012 0011010100 1000010100 0100001001 1001000000 --01000111 0111-10000 -11-111021 -111111111 1111111111 11211
Haplobunodontid 1000100002 0001010000 0000000000 01010101-1 1001000000 000100001- -1101000-- 01---11121 0110011111 1111111110 11200
Cebochoerid 1000010002 0000010000 0000000000 01010----1 -00----000 0----1-010 01110----- -1---11121 --1111---- ---------- -1200
Raoellid --01000002 0000000000 1100000000 1-0-000--1 100------- 01-----00- -1-------- ---0-01-2- -------0-1 111111---- -----

;

end;



PART III. Consensus Tree

The following is a consensus tree obtained by heuristic search algorithms using PAUP Version 4.0b8 software (Swofford, 1998) with the following settings: random addition sequence (1000 replications); Tree Bisection and Reconnection (TBR) branch swapping; steepest descent option not in effect; branches collapsed (creating polytomies) if maximum branch length is zero; 'MulTrees' option in effect; trees unrooted; uninformative characters excluded; eight characters ordered; Arctocyon as outgroup.


P A U P *

Version 4.0b8 for Macintosh (PPC/Altivec)

Wednesday, July 18, 2001 3:39 PM

Processing of file "Artiodactyl-Cetacea" begins...


Data matrix has 29 taxa, 105 characters

Valid character-state symbols: 012

Missing data identified by '-'

Gaps identified by '-', treated as missing


Processing of file "Artiodactyl-Cetacea" completed.
Character-exclusion status changed:

10 characters excluded

Total number of characters now excluded = 10

Number of included characters = 95


Outgroup status changed:

1 taxon transferred to outgroup

Total number of taxa now in outgroup = 1

Number of ingroup taxa = 28


Heuristic search settings:

Optimality criterion = maximum parsimony

Character-status summary:

10 characters are excluded

Of the remaining 95 included characters:

8 characters are of type 'ord' (Wagner)

87 characters are of type 'unord'

All characters have equal weight

All characters are parsimony-informative

Starting tree(s) obtained via stepwise addition

Addition sequence: random

Number of replicates = 1000

Starting seed = 519105644

Number of trees held at each step during stepwise addition = 1

Branch-swapping algorithm: tree-bisection-reconnection (TBR)

Steepest descent option not in effect

Initial 'MaxTrees' setting = 20800 (will be auto-increased by 100)

Branches collapsed (creating polytomies) if maximum branch length is zero

'MulTrees' option in effect

Topological constraints not enforced

Trees are unrooted
Heuristic search completed

Total number of rearrangements tried = 67968050

Score of best tree(s) found = 281

Number of trees retained = 38

Time used = 00:01:30.1
Tree-island profile:

First Last First Times

Island Size tree tree Score replicate hit

----------------------------------------------------------------------

1 38 1 38 281 1 860

2 38 - - 282 4 140*


Note(s):

* Multiple hits on islands of unsaved trees may in fact represent different islands


Strict consensus of 38 trees:
/------------------------------------------------------------------------- Arctocyon

|

| /------------- Hyopsodus



| |

| /----------------------------------------------------+ /------- Phenacodus

| | \-----+

| | \------- Meniscotherium

| |

| | /------------------------------------------------------------ Andrewsarchus



| | |

| | +------------------------------------------------------------ Eoconodon

| | |

| | | /------------- Hapalodectes



\------+ | |

| | +------------- Dissacus

| | |

| | +------------- Ankalagon



| | |

| | +------------- Sinonyx

| +----------------------------------------------+

| | +------------- Pachyaena

\-----+ |

| | /------- Mesonyx

| +-----+

| | \------- Harpagolestes

| |

| \------------- Synoplotherium



|

| /------- Pakicetus

| /---------------------------------------------+

| | \------- Ambulocetus

| |

| | /---------------------------------------------- D pakistanensis



| | |

\------+ | /--------------------------------- D secans

| | |

| | | /--------------------------- Archaeotherium



| | /------+ |

| | | | | /-------------------- Elomeryx

\------+ | \-----+ |

| | | | /------- Hippopotamus

| | \------+ /-----+

| | | | \------- Hexaprotodon

| | \------+

| | \------------- Sus

| |

\-----+ /------------- Agriochoerus



| |

| /------+ /------- Poebrotherium

| | \-----+

| | \------- Tragulus

| /------+

| | +-------------------- Haplobunodontid

| | |

\------------+ \-------------------- Cebochoerid



|

\--------------------------- Raoellid




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