Supporting Online Material for

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1 Supporting Online Material for Laonastes and the Lazarus Effect in Recent Mammals Mary R. Dawson,* Laurent Marivaux, Chuan-kui Li, K. Christopher Beard, Grégoire Métais *To whom correspondence should be addressed. This PDF file includes: Materials and Methods SOM Text Fig. S1 References Published 10 March 2006, Science 311, 1456 (2006) DOI: /science

2 Supplementary online material Materials and Methods: Data were managed by MacClade 3.04 (1). Phylogenetic reconstructions were performed by PAUP* 4.0 beta 10 Win (2). As the data set contained too many taxa for executing an exact search (Branch and Bound option), heuristic search methods (Hsearch) with a random step-wise addition (100 replications with randomized input order of taxa) and tree bisection-reconnection (TBR) branch swapping options were applied. The multistate characters were considered as ordered (labeled by an asterisk * ) if changes from one state to another required passing through intermediate states. With such an ad hoc assumption, character state assignments do not convey a priori judgments about character polarity (no state considered plesiomorphic or apomorphic a priori). For instance, in the case of a character showing three states (0,1,2), the ancestral state could be any of the three states (unconstrained parsimony). Considering ordered characters simply means that to get state 0 to state 2, or the reverse, involves an intermediate state 1 (ordered morphoclinal transformations). This enforces a gradualist perspective on morphological evolution. Selected characters and character states are after Marivaux et al. (3) and Wible et al. (4). Character descriptions: Incisor enamel microstructure 1. *Prisms per Hunter-Schreger Bands (HSB): (0) 1; (1) 1-3; (2) 2-4; (3) 3-5; (4) 4-6; (5) greater than *IPM crystallites arrangement in PI: (0) sheath surrounding prisms; (1) parallel; (2) acute angle, anastomosing; (3) perpendicular. 3. IPM thickness in PI: (0) equal to or thicker than prisms; (1) thinner than prisms. 4. *Band inclination relative to EDJ: (0) 0 0 ; 1) <10 0 ; (2) ; (3) ; (4) ; (5) Dental characters 5. Crowns of cheek teeth: (0) brachydont; (1) some unilateral hypsodonty; (2) slightly elevated crowns; (3) hypsodont. 6. Roots of upper molars: (0) 3; (1) 2; (2) 4; (3) one fused root. 7. Roots of lower molars: (0) 2; (1) 3; (2) 4; (3) one fused root. 8. Upper cheek tooth rows: (0) parallel, (1) convergent anteriorly. 9. P4-M3: (0) subequal in size; (1) size increases posteriorly; (2) size greatest at M1-2; (3) size increases anteriorly. 10. p4-m3: (0) subequal in size; (1) size increases posteriorly; (2) size greatest at m1-2; (3) size increases anteriorly. 11. Main cheek teeth cusps/cuspids (0) bunodont; (1) crests present but low; (2) multiple high lophs/lophids present; (3) lophodont. Upper premolars 12. *Number of permanent upper premolars: (0) 2; (1) 1; (2) Labial cusp(s) of P4: (0) single; (1) double, subequal in size. 14. *Anterior and posterior ridges of P4: (0) weak or incomplete; (1) distinct but low; (2) as high as protoloph and metaloph. 15. *P4 hypocone: (0) minute to absent; (1) small; (2) large.

3 16. P4 protoconule: (0) present; (1) absent. 17. *P4 metaconule: (0) present; (1) reduced; (2) indistinct to absent. 18. *Protoloph on P4: (0) absent; (1) incomplete; (2) complete. 19. *Metaloph on P4: (0) absent; (`1) incomplete; (2) complete; (3) submerged in posteroloph. 20. *Mesostyle on P4: (0) absent; (1) small; (2) large. Upper molars 21. Labial cingulum: (0) present; (1) absent. 22. *Hypocone: (0) absent; (1) small; (2) large, subequal to protocone. 23. *Hypocone position: (0) more lingual than protocone; (1) same level as protocone; (2) more labial than protocone. 24. Anterior arm of hypocone: (0) absent; (1) present. 25. *Mesostyle: (0) absent; (1) small; (2) large. 26. *Parastyle: (0) absent; (1) small; (2) large. 27. *Anterostyle: (0) absent; (1) small; (2) large. 28. *Anteroloph: (0) weak or absent; (1) low; (2) high and connected to protocone. 29. *M1-2 metaconule: (0) strong; (1) reduced; (2) indistinct (included in the mure); (3) absent. 30. Metaconule-hypocone connection: (0) absent; (1) present. 31. Metaconule-protocone connection: (0) absent; (1) present. 32. *Mesoloph: (0) absent; (1) from mesostyle on lingual side and extending lingually; (2) reaches lingual side. 33. Protoloph (protolophule II): (0) absent; (1) present. 34. Metaloph: (0) connected to metaconule; (1) connected to protocone; (2) connected to hypocone; (3) joins posteroloph; (4) absent (or submerged in posteroloph). 35. Neoendoloph (posterior outgrowth of the protocone): (0) absent; (1) present. 36. *Posteroloph: (0) weak or absent; (1) distinct, but low; (2) even with or higher than metaloph. 37. *M1-2 protoconule: (0) large; (1) reduced; (2) absent (or submerged in protoloph). 38. Hypoflexus: (0) absent or shallow; (1) deep. Lower premolar, p4 39. Size of p4: (0) smaller than m1; (1) equal to or greater than m *Talonid width of p4: (0) narrower than or equal to trigonid; (1) slightly wider than trigonid; (2) much wider than trigonid. 41. Hypolophid: (0) absent; (1) present. 42. Paraconid: (0) present; (1) absent. 43. Metaconid/protoconid position: (0) opposed; (1) protoconid posterior; (2) metaconid posterior. 44. Hypoconulid: (0) absent; (1) present. 45. Hypoconid: (0) present; (1) absent. 46. Mesoconid: (0) absent; (1) present. 47. *Ectolophid: (0) absent; (1) incomplete; (2) complete. 48. *Metalophulid I: (0) absent; (1) incomplete, unconnected to metaconid; (2) complete. 49. *Metalophulid II (posterior arm of protoconid): (0) absent; (1) incomplete, unconnected to metaconid; (2) complete. 50. Anterior cingulid: (0) absent; (1) present. 51. *Posterior arm of metaconid (metastylar fold): (0) absent; (1) low, weak; (2) well developed, high.

4 Lower molars 52. Paraconid: (0) reduced; (1) absent. 53. *Anterolophid (anterocingulid): (0) absent; (1) low; (2) well developed. 54. Metalophulid I: (0) complete (ancestral paralophid); (1) weak to absent. 55. *Anteroconid: (0) absent; (1) small in anterolophid; (2) well developed. 56. Mesostylid: (0) absent; (1) present. 57. Ectostylid: (0) absent; (1) present. 58. Mesoconid: (0) small to absent; (1) simple cuspid. 59. *Ectolophid: (0) absent; (1) anteriorly incomplete; (2) complete, reaches protoconid. 60. *Mesolophid: (0) absent; (1) short; (2) well developed, reaches the lingual side. 61. Protoconid-metaconid position: (0) opposed; (1) protoconid posterior. 62. Direction of metalophulid II (posterior protoconid arm): (0) directed toward metaconid; (1) oblique, extending backward; (2) extending anteriorly toward metaconid. 63. *Metalophulid II (posterior arm of protoconid): (0) well developed; (1) weak; (2) small to absent. 64. *Hypolophid: (0) absent, (1) low, interrupted labially, (2) well developed. 65. *Anterior arm of hypoconid: (0) absent; (1) connects weakly to mesoconid; (2) well developed. 66. Entoconid / hypoconid position: (0) opposed; (1) entoconid anterior. 67. *Hypoconulid: (0) strong, inflated; (1) «normal» (simple cuspid); (2) reduced, submerged into the posterolophid; (3) absent. 68. Entoconid hypoconid connection by posterolophid: (0) present; (1) absent. Cranial characters 69. *Incisive foramina: (0) closer to incisors; (1) at mid rostrum; (2) nearly as long as diastema. 70. Nasal: (0) broadest posteriorly; (1) nearly parallel; (2)broadest anteriorly. 71. Infraorbital foramen: (0) sciuromorphous; (1) protrogomorphous; (2) hystricomorphous; (3) myomorphous. 72. Palatine on palate: (0) anterior extent to M1; (1) anterior to M1; (2) posterior to M Posterior margin of palate: (0) at or in front of M3; (1) posterior to M Orbital wing of palatine: (0) small, posterior to molars: (1) prolonged anteriorly. 75. Sphenopalatine foramen: (0) within maxilla; (1) between maxilla and palatine; (2) between maxilla and frontal; (3) between maxilla and lacrimal. 76. Lacrimal facial process: (0) small; (1) substantial. 77. Jugal: (0) contacts lacrimal; (1) has process anterior to orbit but does not contact lacrimal; (2) is entirely ventral to orbit. 78. Nasolacrimal foramen: (0) between lacrimal and maxilla; (1) within lacrimal; (2) within maxilla. 79. Lateral vacuity of nasolacrimal duct: (0) absent; (1) present. 80. Orbital pocket of lacrimal: (0) absent; (1) present. 81. Orbits: (0) anterior extent over P4 or more anterior; (1) more posteriorly. 82. Orbit size: (0) less than 15% skull length; (1) greater than 20% skull length. 83. Supraorbital crest: (0) absent; (1) present. 84. Postorbital process: (0) absent; (1) on frontal; (2) on parietal and squamosal. 85. Frontoparietal suture: (0) narrow, V-shaped; (1), flat; (2) broad, U-shaped. 86. Temporal lines: (0) meet anteriorly to form sagittal crest; (1) meet posteriorly to form sagittal crest; (2) sagittal crest absent. 87. Interparietal: (0) absent; (1) present. 88. Hamulus-bulla relationship: (0) hamulus distant from bulla; (1) extends to or nearly to bulla. 89. Left and right optic foramina: (0) separate; (1) confluent. 90. Orbital process of alisphenoid: (0) significant; (1) greatly reduced.

5 91. Alisphenoid-frontal contact: (0) present; (0) absent. 92. Alisphenoid-parietal contact: (0) present; (1) absent. 93. Pterygoid fossa: (0) shallow; (1) deep. 94. *Neurovascular canal: (0) absent; (1) open groove; (2) covered canal. 95. Sphenopalatine vacuity: (0) absent; (1) present. 96. Foramen ovale: (0) within alisphenoid; (1) between alisphenoid and petrosal or ectotympanic. 97. Foramen ovale accessorius: (0) absent; (1) present. 98. Masticatory and buccinator foramina: (0) absent; (1) present. 99. Ectopterygoid crest: (0) short, anterior to foramen ovale; (1) long, extends beyond foramen ovale Alisphenoid tympanic process posterior to foramen ovale: (0) absent; (1) present Alisphenoid canal: (0) present; (1) absent Glenoid fossa: (0) near anterior extent of ear region; (1) well anterior to ear region Postglenoid foramen: (0) within squamosal; (1) between squamosal and ectotympanic or petrosal Anteromedial shelf of petrosal: (0) ridge-like; (1) flattened; (2) separated from promontorium Transpromontorial groove for internal carotid artery: (0) present; (1) absent Groove for stapedial artery on promontorium: (0) present; (1) absent Stapedial artery: (0) ventral to fenestra cochleae; (1) partially shielding fenestra Facial nerve: (0) occupies groove in middle ear; (1) enclosed in canal Fenestra cochleae: (0) facing posteroventrally ;(1) turning laterally Lateral section of caudal tympanic process of petrosal: (0) with prolonged posterior horizontal shelf; (1) forms vertical wall Mastoid of petrosal: (0) not inflated; (1) inflated Mastoid exposure on occiput: (0) present; (1) nearly or completely absent *Petrosal exposure dorsal to external acoustic meatus: (0) absent; (1) present; (2) inflated Osseous external auditory canal: (0) absent; (1) present Malleus/incus fusion: (0) absent; (1) present Tympanic process of basioccipital: (0) absent or weak; (1) strong Paracondylar process: (0) short; (1) long, curving under bulla; (2) moderately short but prominent. Mandibular characters 118. Mental foramina: (0) two or more; (1) one Mental foramen position: (0) anterior foramen below p4; (1) below diastema; (2) on dorsal side of diastema Mental foramen location on the dentary: (0) mesial; (1) dorsal *Coronoid process: (0) large; (1) reduced, subequal to condylar process; (2) small; (3) absent *Mandibular condyle height: (0) much higher than occlusal surface; (1) lower but above occlusal surface; (2) even with occlusal surface Angular process: (0) origin in plane of body (sciurognathous); (1) origin lateral to plane of body (hystricognathous) *Anterior edge of masseteric fossa: (0) extends below m3; (1) below m2; (2) below m1; (3) below p Dorsal margin of masseteric fossa: (0) inclined; (1) horizontal Mandibular foramen: (0) at level of tooth row or higher; (1) lower than tooth row *Length of lower incisor: (0) long, to or nearly to condyle; (1) long, into lateral tubercle on ascending ramus; (2) shorter, to below m1-m3.

6 Postcranial characters 128. Entepicondylar foramen of humerus: (0) present; (1) absent Distal end humerus: (0) wide; (1) narrow *Deltoid process of humerus: (0) shallow ridge; (1) strong ridge; (2) prominent process Femoral neck (0) short and broad; (1) long and narrow Femoral lesser trochanter: (0) medially directed; (1) posteromedially directed; (2) posteriorly directed Femoral third trochanter: (0) close to greater trochanter; (1) more distal; (2) halfway or more down shaft Medial trochlea of astragalus: (0) low, broad; (1) high, narrow *Astragalar neck: (0) short (neck ratio: length divided by width <1); (1) moderate (length divided by width subequal to 1); ( (2) long (length divided by width >1) Lateral astragalar trochlear border: (0) higher than medial border; (1) as high as medial border. Character matrix: #NEXUS [ File saved by NDE version 0.5.0, Sun Oct 16 14:43: ] BEGIN TAXA; DIMENSIONS NTAX=20; TAXLABELS Rhombomylus Alagomys Cocomys Paramys Reithroparamys Sciuravus Tamquammys Tataromys Yuomys

7 Tsaganomys Pectinator Hystrix Thryonomys Erethizon Dasyprocta Anomalurus Fallomus Diatomys Laonastes Marmota ; ENDBLOCK; BEGIN CHARACTERS; DIMENSIONS NCHAR=136; FORMAT DATATYPE=STANDARD MISSING=? GAP=- SYMBOLS[*]= " "; OPTIONS MSTAXA=POLYMORPH; MATRIX Rhombomylus ?? ? ??? 000?01?10? 10010? Alagomys ??1 0???0? ?0{01} ?????????????????????????????????????????????????111 0??1???????????? Cocomys 20021?? ? ? ??????????? Paramys ??

8 Reithroparamys {01}0011{01} ??00? ?00??00?0??? ? Sciuravus {01} {01} 1{02}00000? ?? ?0? ?0?0?{01} ????????? Tamquammys 3{12}041?? ?? 2????????????????????????????????????????????????????1???????????? Tataromys????{03} {01}22010? ?? ? ? 00??1??1?1 1021? ??????{01}11 Yuomys????0??? {12} ? 2??????????????????????????????????????????????110??010??????????? Tsaganomys ?1?2?? 1{01} {01}0000? ?10?2?2?? ? ?00? ?11? ? ????????? Pectinator????3??011 21? ? ? 01? ?? {12} ? ?1?1 1021? ????????? Hystrix 510{03} ?11???1 01? ?100 Thryonomys ??? 0100? ? ?11??? ??? ????????? Erethizon ?20? ? {01}00 10{01} Dasyprocta {01}11211? ???? Anomalurus 11?{03} ? 1200? {12} ?01011? ? ??0201{12} Fallomus 32140{02}2? ? ? {01} {12}0?? 2??????????????????????2????????????????????????????????2????????? Diatomys ? ? ? {01}0030?? 2????????? 1??????????????????????????????????? ?2?????????

9 Laonastes {13}{13} ? ? ?000 00{12}{01} ?101?? ? ??????? Marmota???? ??02111? {13} ??????? ? {01} ; ENDBLOCK; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE=UNORD POLYTCOUNT=MINSTEPS; TYPESET * saved = ord: , unord: ; WTSET * saved = 1: 1-136; ENDBLOCK; BEGIN PAUP; Outgroup Rhombomylus/only; Assume ancstates=standard; ENDBLOCK; log file = Hsearch.out; Hsearch Nreps = 100 addseq = random;

10 Results: P A U P * Version 4.0b10 for 32-bit Microsoft Windows Tue Oct 25 10:45: NOTICE This is a beta-test version. Please report any crashes, apparent calculation errors, or other anomalous results. There are no restrictions on publication of results obtained with this version, but you should check the WWW site frequently for bug announcements and/or updated versions. See the README file on the distribution media for details Processing of file "D:\Laonastes_Matrix.nex" begins... Data matrix has 20 taxa, 136 characters Valid character-state symbols: Missing data identified by '?' Gaps identified by '-' Outgroup status changed: 1 taxon transferred to outgroup Total number of taxa now in outgroup = 1 Number of ingroup taxa = 19 Logging output to file "D:\Hsearch.out". Heuristic search settings: Optimality criterion = parsimony Character-status summary: Of 136 total characters: 43 characters are of type 'ord' (Wagner) 93 characters are of type 'unord' All characters have equal weight 5 characters are parsimony-uninformative Number of parsimony-informative characters = 131 Gaps are treated as "missing" Multistate taxa interpreted as polymorphism Starting tree(s) obtained via stepwise addition Addition sequence: random Number of replicates = 100 Starting seed = Number of trees held at each step during stepwise addition = 1 Branch-swapping algorithm: tree-bisection-reconnection (TBR) Steepest descent option not in effect

11 Initial 'MaxTrees' setting = 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 = Score of best tree(s) found = 609 Number of trees retained = 4 Time used = 0.84 sec Tree-island profile: First Last First Times Island Size tree tree Score replicate hit * * * * * Note(s): * Multiple hits on islands of unsaved trees may in fact represent different islands Processing of file "D:\Laonastes_Matrix.nex" completed.

12 Strict consensus of 4 trees: / Rhombomylus / Alagomys / Paramys Reithroparamys Sciuravus / Tataromys / / Pectinator \ / Fallomus / \ / Diatomys \ \ Laonastes \ \ Yuomys / / Tsaganomys / Hystrix / \ \ Dasyprocta \ Erethizon \ Thryonomys \ Anomalurus \ Marmota Cocomys \ Tamquammys Tree description: Unrooted tree(s) rooted using outgroup method Optimality criterion = parsimony Character-status summary: Of 136 total characters: 43 characters are of type 'ord' (Wagner) 93 characters are of type 'unord' All characters have equal weight 5 characters are parsimony-uninformative Number of parsimony-informative characters = 131 Gaps are treated as "missing" Multistate taxa interpreted as polymorphism ("min" values for CI, RI, and RC are minimum-possible character lengths)

13 Character-state optimization: Accelerated transformation (ACCTRAN) Tree length = 609 Consistency index (CI) = Homoplasy index (HI) = CI excluding uninformative characters = HI excluding uninformative characters = Retention index (RI) = Rescaled consistency index (RC) = Figures: Figure S1. Diatomys shantungensis, IVPP12692, lateral view of specimen, anterior to right. References: S1. W. P. Maddison, D. R. Maddison, MacClade, Analysis of Phylogeny and Character Evolution (Sinauer Associates, Inc, Sunderland, Mass., 1992). S2. D. L. Swofford, PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. (Sinauer Associates, Sunderland, Massachusetts, 2002). S3. L. Marivaux, M. Vianey-Liaud, J.-J. Jaeger, Zool. J. Linnean Soc. 142, 105 (2004). S4. J. R. Wible, Y. Wang, C. Li, M. R. Dawson, Annals of Carnegie Museum 74, 91 (2005).