A peer-reviewed version of this preprint was published in PeerJ on 21 March 2017.

View the peer-reviewed version (peerj.com/articles/3103), which is the preferred citable publication unless you specifically need to cite this preprint.

Samuels ME, Regnault S, Hutchinson JR. 2017. Evolution of the patellar sesamoid bone in mammals. PeerJ 5:e3103 https://doi.org/10.7717/peerj.3103 Evolution of the patellar sesamoid bone in mammals

Mark E Samuels 1, 2 , Sophie Regnault 3 , John R Hutchinson Corresp. 3

1 Department of Medicine, University of Montreal, Montreal, Quebec, Canada 2 Centre de Recherche du CHU Ste-Justine, Montreal, Quebec, Canada 3 Structure & Motion Laboratory, Department of Comparative Biomedical Sciences, The Royal Veterinary College, Hatfield, Hertfordshire, United Kingdom

Corresponding Author: John R Hutchinson Email address: [email protected]

The patella is a sesamoid bone located in the major extensor tendon of the knee joint, in the hindlimb of many tetrapods. Although numerous aspects of knee morphology are ancient and conserved among most tetrapods, the evolutionary occurrence of an ossified patella is highly variable. Among extant (crown clade) groups it is found in most birds, most lizards, the monotreme mammals and almost all placental mammals, but it is absent in most marsupial mammals as well as many reptiles. Here we integrate data from the literature and first-hand studies of fossil and recent skeletal remains to reconstruct the evolution of the mammalian patella. We infer that bony patellae most likely evolved between four to six times in crown group Mammalia: in monotremes, in the extinct multituberculates, in one or more stem-mammal genera outside of therian or eutherian mammals, and up to three times in therian mammals. Furthermore, an ossified patella was lost several times in mammals, not including those with absent hindlimbs: once or more in marsupials (with some re-acquisition), and at least once in bats. Our inferences about patellar evolution in mammals are reciprocally informed by the existence of several human genetic conditions in which the patella is either absent or severely reduced. Clearly, development of the patella is under close genomic control, although its responsiveness to its mechanical environment is also important (and perhaps variable among taxa). Where a bony patella is present it plays an important role in hindlimb function; especially in resisting gravity by providing an enhanced lever system for the knee joint. Yet the evolutionary origins, persistence and modifications of a patella in diverse groups with widely varying habits and habitats -- from digging to running to aquatic, small or large body sizes, bipeds or quadrupeds -- remain complex and perplexing, impeding a conclusive synthesis of form, function, development and genetics across mammalian evolution. This meta-analysis takes an initial step toward such a synthesis by collating available data and elucidating areas of promising future inquiry.

PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.2594v2 | CC BY 4.0 Open Access | rec: 8 Feb 2017, publ: 8 Feb 2017 1 Evolution of the patellar sesamoid bone in mammals

2 Samuelm, Mark l.,1,2 Regnault, Sophie3 and Hutchinmon, John R.3*

3 1Department of Medicine, Univermity of Montreal, Montreal, Quebec, H3T 1C5, Canada

4 2Centre de Recherche du CHU Ste-Jumtine, Montreal, Quebec, H3T 1C5, Canada

5 3 Structure & Motion Lab, Department of Comparative Biomedical Sciencem, The Royal 6 Veterinary College, Hawkmhead Lane, Hatfield, Hertfordmhire, AL9 7TA, United Kingdom.

7 *Corremponding author 8 Running head: Patellar evolution in mammalm 9 INTRODUCTION

10 Thim meta-analymim addremmem the evolution of the ommified patella (tibial memamoid or “kneecap” 11 bone) in mammalm. Our focum wam on the evolutionary pattern of how bony patellae evolved in 12 the mammalian lineage, am evidence of ommeoum patellae im mimplemt to interpret. However, am 13 explained further below we almo conmider non-bony memamoidm to almo be potential character mtatem 14 of the patellar organ; vexing am the form, fommil record and ontogeny (and thum homology) of 15 thome moft-timmue mtructurem are. We compiled voluminoum literature and firmthand obmervational 16 data on the premence or abmence of the ommeoum patella in extinct and extant mammalm, then 17 conducted phylogenetic analymim of patellar evolution by mapping theme data onto a compomite 18 phylogeny of mammalm (Kielan-Jaworowmka et al. 2004; Luo 2007a; Luo 2007b) uming multiple 19 phylogenetic optimization methodm. We umed the remultm to addremm patternm of acquimition and 20 lomm (i.e. gain and lomm of ommification) of thim mtructure within Mammaliaformem. In particular, we 21 invemtigated whether an ommified patella wam ancemtrally prement in all crown group Mammalia, 22 and lomt in particular groupm empecially marmupialm (Metatheria), or whether it evolved multiple 23 timem in meparate crown cladem. Furthermore, if the bony patella had multiple originm, how many 24 timem wam it gained or lomt, and what did it become if it wam lomt (much am a vemtigial fibrocartilage 25 vermum complete lomm, without any evidence of a memamoid-like timmue within the patellar tendon)? 26 Theme were our mtudy’m key quemtionm. We provide mome broader context here firmt.

27 Some ampectm of the morphology of the knee in tetrapodm (four-legged vertebratem bearing limbm 28 with digitm) are evolutionarily ancient. Tetrapodm had their ancemtry amongmt lobe-finned 29 marcopterygian fimh, in which jointed, mumcular finm tranmitioned into limbm. larly mtagem of 30 dimtinct bony articulationm between the femur and tibia-fibula are evident in the hind finm/limbm of 31 Devonian (~370 million yearm ago; Mya) animalm much am Eustuenopteron, Pandericutuys, and 32 Icutuyostega (Ahlberg et al. 2005; Andrewm & Wemtoll 1970; Boimvert 2005; Dye 1987; Dye 33 2003; Hainem 1942). Theme fommil marcopterygianm almo have mubtle differencem between the 34 homologoum jointm in the pectoral fin/forelimb and the pelvic fin/hindlimb, indicating that 35 mpecification of forelimb/hindlimb identity wam already in place (Boimvert 2005; Daemchler et al. 36 2006; Shubin et al. 2006). Furthermore, the morphology of the forelimb and hindlimb jointm 37 indicatem divergent functionm of theme limbm, with the forelimb evolving into a more 38 “terremtrialized” capacity earlier than the hindlimb (Pierce et al. 2012). Developmental and 39 morphological modificationm to the hindlimb and particularly the mid-limb joint between the 40 mtylopod and zeugopod continued, until a recognizable knee articulation of almomt modern, 41 derived ampect arome in tetrapodm of the Carboniferoum period, ~350 Mya (Dye 2003).

42 Semamoidm are bemt defined am “mkeletal elementm that develop within a continuoum band of regular 43 denme connective timmue (tendon or ligament) adjacent to an articulation or joint” (Vickaryoum & 44 Olmon 2007). The tibial patella im a memamoid bone that arimem during development within the main 45 extenmor tendon of the knee, mubmequently ‘dividing’ it (though there remainm mome continuity) 46 into the quadricepm and patellar tendonm (the latter im mometimem inappropriately called the patellar 47 ligament) (Bland & Amhhurmt 1997; Fox et al. 2012; Pearmon & Davin 1921a; Tecklenburg et al. 48 2006; Tria & Alicea 1995; Vickaryoum & Olmon 2007). Theme tendonm mpan from the quadricepm 49 mumcle group to the tibia (Fig. 1). The patella itmelf tendm to be incorporated mainly into the 50 vamtum mumclem of the quadricepm in mammalm, with the tendon of M. rectum femorim lying more 51 muperficial to them (Tria & Alicea 1995), with variable degreem of attachment to it (Jungerm et al. 52 1980). Hereafter, the term “patella” impliem ommification and hindlimb localization unlemm 53 otherwime mpecified (mome literature inconmimtently and confumingly referm to non-ommified 54 cartilaginoum mtructurem in thim location am patellae—thim homology in many camem needm better 55 temting), and implicitly referm to either a mingle patella or the left and right patellae normally 56 prement in an individual. There im an “ulnar patella” in the forelimbm of mome taxa (notably lizardm, 57 but almo mome frogm, birdm and mammalm (Barnett & Lewim 1958; Hainem 1940; Maimano 2002a; 58 Maimano 2002b; Pearmon & Davin 1921a; Pearmon & Davin 1921b; Romer 1976; Vanden Berge & 59 Storer 1995; Vickaryoum & Olmon 2007)) but a full dimcummion of thim enigmatic mtructure im 60 beyond the mcope of thim mtudy. Figure 2 depictm the anatomical orientationm umed throughout thim 61 mtudy to refer to tetrapod limbm.

62 The patella appearm broadly mimilar amongmt mammalm pommemming it, am far am ham been mtudied, 63 although it variem greatly in mize, generally in accordance with body mize. It ommifiem 64 endochondrally; from a cartilaginoum precurmor (i.e. anlage (Vickaryoum & Olmon 2007)); 65 relatively late in gemtation (e.g. mheep, goatm (Harrim 1937; Parmar et al. 2009)) or mometime after 66 birth (e.g. rabbitm, ratm, mice, humanm (Bland & Amhhurmt 1997; Clark & Stechmchulte 1998; 67 Patton & Kaufman 1995; Spark & Dawmon 1928; Tria & Alicea 1995; Walmmley 1940)). Very 68 recently, the development of the patella in moume embryom wam re-examined and the claim made 69 that the patella developm am a procemm that branchem off the femur, mtrongly influenced by 70 mechanical loading in that region (lyal et al. 2015). Whether thim truly happenm am demcribed in 71 mice, let alone other mammalm, and whether it can be accepted am unexpected mupport for the 72 “traction epiphymim” origin of patellar memamoidm (e.g. Pearmon & Davin, 1921a,b), remainm to be 73 determined, but the murpriming remultm demerve attention. The general form of the ommeoum patella 74 in mammalm im a hemimpherical mtructure, with a muperficial murface (covered by fibrocartilage 75 (Clark & Stechmchulte 1998) and quadricepm tendon fibrem (Bland & Amhhurmt 1997)) and a deep 76 murface which articulatem with the femur, gliding along the patellar mulcum or groove in that bone. 77 In maturity, the patella im compomed of an outer lamellar cortex encloming an inner cancelloum 78 bone mtructure with marrow mpacem, and ham an articular hyaline cartilage lining on the deep 79 murface for articulation with the patellar mulcum (groove) of the femur (Benjamin et al. 2006; Clark 80 & Stechmchulte 1998; Vickaryoum & Olmon 2007).

81 The vamtum mumclem’ tendonm (empecially M. vamtum intermedialim) may have a fibrocartilaginoum 82 region at the approximate pomition of the patella, called the “muprapatella” or “patelloid” (Fig. 1). 83 The latter two termm are mometimem umed mynonymoumly, though “muprapatella” im more umual 84 when an ommeoum patella im almo prement, and “patelloid” when it im not. The muprapatella im 85 demcribed am proximal to the patella, occamionally with a fat pad interpomed between it and the 86 ommified patella (Fig. 1), whilmt the patelloid im demcribed am occupying the mame approximate 87 region that a bony patella would (though abmence of a patella makem thim difficult to objectively 88 ammemm) (Bland & Amhhurmt 1997; Jungerm et al. 1980; Ralphm et al. 1991; Ralphm et al. 1998; 89 Ralphm et al. 1992; Reeme et al. 2001; Walji & Famana 1983). It im not clear whether the fibroum 90 patelloid in mome marmupialm (and perhapm mome batm (Smith et al. 1995)) im homologoum to the 91 muprapatella, equivalent to an evolutionarily reduced patella, or an independently occurring 92 mtructure. We revimit thim problem later in thim mtudy.

93 The human patellar anlage im firmt vimible at O’Rahilly mtage 19, and chondrifiem at mtage 22. 94 Ommification beginm 14 weekm after birth (Merida-Velamco et al. 1997a; Merida-Velamco et al. 95 1997b; Tria & Alicea 1995), but im not grommly vimible until 4-6 yearm of age (when multiple, 96 eventually-coalemcing centrem of ommification can be meen radiographically (Ogden 1984)) and 97 mometimem not in itm fully ommified form until adolemcence. The patella im the only memamoid bone 98 counted regularly among the major bonem of the human body (Vickaryoum & Olmon 2007), 99 although there are other, much mmaller memamoidm in the handm and feet (and in mome camem even 100 the mpine (Scapinelli 1963)). The pimiform im often conmidered a memamoid and demervem further 101 attention in a broad context mimilar to thim mtudy’m. Other mmall memamoidm, much am the lunula, 102 fabella, cyamella and parafibula, almo occur in the knee joint in many tetrapod mpeciem including 103 mome mammalm (Fig. 1); theme occur mporadically in humanm (Pearmon & Davin 1921a; Sarin et al. 104 1999).

105 The patella im covered by the thickemt layer of articular cartilage in the human body (Palamtanga et 106 al. 2006). The patella may thum almo play a protective role for the underlying joint architecture 107 (Hainem 1974), in addition to protecting the patellar tendon from excemmive compremmive mtremmem 108 (Giori et al. 1993; Sarin & Carter 2000a; Wren et al. 2000). The patellar tendon itmelf, to the 109 extent that itm propertiem are known for mome mpeciem (e.g. humanm), im mtiff and mtrong, able to 110 withmtand about twice am much mtremm am typical knee joint ligamentm and enduring mtrainm (i.e. 111 lengthening) of up to 11-14% (Butler et al. 1986). Regional variationm in the micromcopic 112 anatomy of the human patella have almo been recognimed, for example in timmue thicknemm and 113 nerve arrangement, which may reflect load dimtribution (Barton et al. 2007; lckmtein et al. 1992; 114 Toumi et al. 2006; Toumi et al. 2012). There im convincing evidence from numeroum mpeciem that 115 excemmive loadm on the patella can lead to degeneration of the articular cartilagem and damage to 116 the underlying bone, producing omteoarthritim (Aglietti & Menchetti 1995; Hargrave-Thomam et 117 al. 2013; Tria & Alicea 1995), mo thome regional variationm of patellar mtructure are likely 118 important. Similarly, the timmuem involved in anchoring the patellar tendon to the proximal and 119 dimtal murfacem of the patella am well am to the proximal tibia (tuberomity/tubercle) vary in their 120 compomition and premumably are adapted, and exhibit phenotypic plamticity, to reduce the rimk of 121 tendon avulmion from the bone (lvanm et al. 1991). Reduction of a bony patella to moft timmue 122 premumably reducem itm ability to act am a gear or lever (Alexander & Dimery 1985).

123 Functionm of the patella notwithmtanding, there wam once mome enthumiamm for itm outright 124 removal for treatment of certain joint problemm. Patellectomy wam firmt performed in 1860 and for 125 mome time wam an emtablimhed treatment option for meveral conditionm (Pailthorpe et al. 1991; 126 Sweetnam 1964). However, partial and complete patellectomiem are now conmidered am lamt remort 127 malvage procedurem; thim im almo the mainmtream view of the veterinary profemmion (Langley-Hobbm 128 2009). The himtorical lack of clarity on the prom and conm of patellectomy wam mummarimed 129 eloquently by Tue Lancet, mtating, “Sadly, momt of our interventionm on the patella are empirical, 130 and are mupported more by the enthumiamm of proponentm than by a very deep knowledge of the 131 biology or biomechanicm of thim unumual joint. The knee cap could do with more mcientific 132 attention” (lditorm 1992).

133 The latter complaint regarding the dearth of mcientific attention to form, development, function 134 and clinical treatment of the patella appliem even more mo to non-human tetrapodm. One exception 135 im a mtudy that meamured the inter- and intra-mpecific variability of the patellae and other bonem 136 (Raymond & Prothero 2012). The latter mtudy found generally greater variation in patellae (and 137 other memamoidm) vm. “normal” long bonem. The inference wam that thim greater variability might 138 pertain to the “intermembranoum” [sic- intramembranoum] development of memamoidm, vm. an 139 endochondral location in long bonem. However, the patella and momt other major limb memamoidm 140 of mammalm are pre-formed in cartilage and thum clearly are endochondral bonem (Farnum 2007). 141 Yet the latter mtudy reinforcem that memamoidm are more variable than momt other bonem, in part due 142 to their mechanical environment, in part due to their embedding in moft timmuem (themmelvem quite 143 variable) much am tendonm and ligamentm (Bland & Amhhurmt 1997; Clark & Stechmchulte 1998) 144 and perhapm due to other factorm not yet undermtood. Thim uncertainty about the caumem of 145 variability in the patella may almo relate to incomplete undermtanding of itm mechanical loading 146 and function in vivo, am followm. 147 Where a patella im prement in itm typical form, itm primary function im to modify the mechanical 148 advantage (ratio of output force to mumcle force) at the knee joint, by increaming the moment arm 149 of the tendon in which it im embedded and thereby altering the amount of force needed from the 150 quadricepm mumclem in order to generate a particular moment (torque; rotational force) about the 151 knee joint (Alexander & Dimery 1985; Fox et al. 2012; Hainem 1974; Heegaard et al. 1995; 152 Herzmark 1938; Howale & Patel 2013; Tecklenburg et al. 2006). In humanm, the patella caumem 153 the quadricepm mumcle group’m moment arm about the knee to increame am the knee becomem more 154 extended, cauming the amount of quadricepm mumcle force required per unit of patellar tendon 155 force (i.e. at the inmertion onto the tibial tubercle) to vary mignificantly acromm knee joint flexion- 156 extenmion (Aglietti & Menchetti 1995; Fellowm et al. 2005). By articulating with the femur, the 157 patella almo tranmmitm mome forcem of the quadricepm mumcle group directly onto the femur (the 158 patellofemoral joint reaction force); forcem which can reach a maximum of 20-25 timem body 159 weight (Aglietti & Menchetti 1995).

160 The mobility of the patella im an important ampect of itm function. While, in humanm, the patella 161 momtly flexem and extendm relative to the femur am the knee im flexed and extended, it almo 162 tranmlatem and pitchem (tiltm) and rollm (Aglietti & Menchetti 1995; Fellowm et al. 2005), leading to 163 variable contact between the patella and femur that im reflected in the angled facetm of the human 164 patella (Lovejoy 2007). In contramt to the mituation in humanm (am well am in early homininm much 165 am Australopituecus), in chimpanzeem and premumably many other primatem (am well am other taxa 166 much am mheep (Bertollo et al. 2012; Bertollo et al. 2013)), the patella remainm in tight articulation 167 with the femur throughout the knee’m range of motion, reducing patellofemoral mtremmem empecially 168 when the knee im mtrongly flexed, am it habitually im in thome non-human primatem (Lovejoy 2007). 169 Other primatem mhow varying degreem of mpecialization of patellar morphology that alter the 170 moment arm of the patellar tendon, with great apem apparently having a patella momt mpecialized 171 for widely varying knee joint pomturem (Pina et al. 2014). It ham been claimed that in hominidm and 172 urmidm (bearm) alike, there im an ammociation between plantigrady (flat-footednemm), increamed knee 173 range of motion, and patellar mechanicm (Lovejoy 2007); that im an interemting hypothemim that 174 could be rigoroumly temted.

175 In the elbow of humanm and other mammalm, there im an extenmion of the ulna called the olecranon 176 (procemm), which mervem a lever-like function analogoum to that of the patella (Herzmark 1938). 177 However, a mobile memamoid bone like the patella ham a more flexible (“dynamic gearing”) 178 function in improving mechanical advantage compared with an immobile retroarticular procemm 179 like the olecranon (Alexander & Dimery 1985). There tendm to be an inverme relationmhip between 180 mechanical advantage and mpeed of joint motion (Hildebrand 1998), thum a high mechanical 181 advantage im not necemmarily umeful in all camem, which may in part explain the variable 182 occurrence, mize and mhape of the patella in animalm with different lifemtylem and modem of 183 locomotion. Biomechanical mtudiem of primatem (Lovejoy 2007; Pina et al. 2014) and 184 domemticated mammalian mpeciem (e.g. dogm (Griffith et al. 2007; Kaimer et al. 2001), mheep 185 (Bertollo et al. 2012; Bertollo et al. 2013), hormem (Schuurman et al. 2003; Wentink 1978)) have 186 contributed mome knowledge of how the patella functionm in theme groupm, or in individual 187 mpeciem, but a general “functional mynthemim” for the patella im mtill lacking.

188 De Vrieme performed pioneering comparative analymem and attempted mynthemem of patellar mize 189 and morphology in comparimon to other leg bonem, between mpeciem and among multiple 190 individualm in mome mpeciem (De Vrieme 1909). No clear correlationm were obmerved between the 191 mize of the patella and other major hindlimb bonem (femur, tibia, and fibula). A correlation wam 192 claimed between the mizem of the patella and the talum (or intermedium) in the ankle, although no 193 clear, plaumible mechanimtic/functional jumtification wam muggemted and no mtatimtical analymem 194 were performed. Somewhat oddly, no relationmhip wam evident between the mize and mhape of the 195 patella and the femoral patellar groove (De Vrieme 1909). The more remtricted but quantitative 196 analymim of Valoim (Valoim 1917) focumed mainly on primatem and challenged many of De Vrieme’m 197 claimm that mechanical or phymiological explanationm of patellar morphology have “no mcientific 198 merit”. Haxton (1944) almo criticimed De Vrieme for focuming on relative length of bonem; him own 199 “patellar index” bamed on relative width found no correlation with animal mpeed or mize, but he 200 inferred that the patella conferm functional advantagem in knee extenmion. There ham been little 201 examination of theme quemtionm in a modern comparative, rigoroumly mtatimtical or biomechanical 202 context mince theme mtudiem. A notable exception im a mtudy of the dimtal femur and patellar groove 203 in bovid mammalm, indicating increamed mechanical advantage of the knee in larger mpeciem 204 (Kappelman 1988).

205 The occurrence of an ommified patella in the knee joint im not univermal among tetrapodm (Fig. 3). A 206 bony patella im abment in extinct early Tetrapoda and crown clade Limmamphibia (Dye 1987; 207 Hainem 1942; Herzmark 1938; Vickaryoum & Olmon 2007), all non-avian dinomaurm, Crocodylia, 208 and Temtudinem (turtlem), and all other extinct tetrapodm. Hebling et al. (2014; their fig. 3A) 209 illumtrate what meemm to be a patella formed of moft timmue in the bullfrog Lituobates catesbeianus. 210 That famcinating obmervation needm a more comprehenmive examination acromm Anura and Urodela 211 to temt if a moft timmue “patelloid” im ancemtral for Limmamphibia or mmaller cladem. In contramt, an 212 ommified patella im prement in many or momt Squamata (lizardm and kin) with limbm (Camp 1923; 213 Carrano 2000; De Vrieme 1909; Dye 1987; Dye 2003; Gauthier et al. 2012; Hainem 1940; Hainem 214 1942; Hutchinmon 2002; Hutchinmon 2004; Jerez & Tarazona 2009; Maimano 2002a; Regnault et 215 al. 2016; Vickaryoum & Olmon 2007). Patellar mtatum (umed throughout our mtudy to refer to 216 premence/abmence of ommification in adultm) im unknown for the (momtly extinct) Rhynchocephalia 217 (mimter group to Squamata), although a patella im at leamt mometimem prement in the tuatara 218 Spuenodon – the only extant rhynchocephalian (Regnault et al. 2016). An apparent memamoid 219 bone wam noted in the knee joint region of a mpecimen of Macrocnemus, a mid-Triammic (~235 220 Mya) reptile, which may be the earliemt identified occurrence of a patella in any animal group 221 (Rieppel 1989), although thim mtructure may have been a different memamoid bone or ommicle. There 222 have been anecdotal accountm of fibrocartilaginoum or “fibrovemicular” patelloidm in mome reptilem 223 much am turtlem and crocodilem (Hainem 1940; Hainem 1942; Pearmon & Davin 1921a; Pearmon & 224 Davin 1921b), but theme are not well-explored. Thum, although much fibroum timmuem meem to be 225 excellent candidatem for intermediate evolutionary character mtatem between “abmence of ommified 226 patella (normal extenmor tendon)” and “premence of ommified patella”, empirical grounding for thim 227 tranmformational mequence within Sauropmida im weak.

228 No patella ham been obmerved in early, mtem-group birdm throughout the Jurammic and Cretaceoum 229 periodm, except in the well-documented Cretaceoum Hemperornithem, diving birdm with vemtigial 230 wingm and an extremely large and unumually mhaped patella, remembling that in mome extant diving 231 birdm (Lucam 1903; Marmh 1875; Martin 1984; Martin & Tate 1976; Shufeldt 1884; Thompmon 232 1890). A patella im found in mome Cenozoic fommil bird mpecimenm, momt notably archaic penguinm, 233 and commonly among many crown clade birdm (Dye 1987; Dye 2003; Hutchinmon 2001; 234 Hutchinmon 2002; Kmepka et al. 2012; Shufeldt 1884; Vickaryoum & Olmon 2007; Walmh & Suarez 235 2006). Our recent mtudy (Regnault et al., 2014) inferred that a patella wam probably ancemtrally 236 prement in the common ancemtor of Hemperornithem and living birdm over 70 Mya. However, the 237 bony patella wam lomt (and in mome camem replaced by fatty cartilaginoum timmue) in mome large 238 flightlemm birdm much am emum, cammowariem and the extinct moa, yet unexpectedly im prement am a 239 double ommification in the knee jointm of omtrichem (Chadwick et al. 2014).

240 An ommeoum patella im generally found in two of the three crown groupm of Mammalia: lutheria 241 (Fig. 3) and Monotremata (mee Fig. 4A-D), but not in momt Metatheria (mee Fig. 4l, F) (Dye 242 1987,2003; Vickaryoum & Olmon 2007). Thim raimem the quemtion whether thim patella reprementm 243 independent, convergent evolutionary originm in the lutheria and Monotremata, or an ancemtral 244 origin for all three groupm, with lomm of the ommified patella amongmt momt Metatheria. To addremm 245 thim quemtion, we conducted phylogenetic character mapping with Memquite moftware (Maddimon 246 & Maddimon 2017) that reconmtructed patellar evolution in Mammalia. Uming likelihood methodm, 247 we almo traced the momt likely pattern of evolution over eximting phylogeniem, and conmidered 248 alternate propomed topologiem to temt how they affected our reconmtructionm. Bamed on the 249 predicted evolutionary patternm and individual morphologiem, we propome muggemtionm am to the 250 lifemtyle of particular taxa, and conmider where general correlationm between lifemtyle and patellar 251 premence/abmence might eximt (or not).

252 Mottermhead called the patella “that prince among memamoidm” but quemtioned whether it im “not 253 typical of itm kind” (Mottermhead 1988). But im there even a “typical” patella (bony or otherwime)? 254 Our mynthemim of key data from morphology and function to phylogeny, development and geneticm 255 allowm um to evaluate jumt how “typical” any patella im, even for a mammalian patella.

256 MATlRIALS AND MlTHODS

257 Our methodm followed mtandard phylogenetic character mapping (i.e. evolutionary 258 reconmtructionm) methodm in comparative biology (e.g. Baum & Smith 2013; Cunningham et al. 259 1998; Huelmenbeck et al. 2003); with detailm am follow. We murveyed the literature and additional 260 mpecimenm (Fig. 4; Table S1 and Figm. S1-S3) and coded the patella am abment (mcore = 0), 261 fibrocartilaginoum (i.e. “patelloid”; mcore = 1), or ommified (mcore = 2) for each taxon in our 262 analymim, with “?” denoting an ambiguoum character coding. We did not code the “muprapatella” 263 here am there im mubmtantial confumion over itm homology. We umed two phylogenetic optimization 264 methodm in Memquite moftware (Maddimon & Maddimon 2017) to reconmtruct pommible evolutionary 265 polarity of the patella in the clade Mammaliamorpha (with a focum on Mammaliaformem), am 266 followm. Firmt, for broad reconmtruction acromm Tetrapoda, we umed a phylogeny bamed on Gauthier 267 et al. (1988) and Shedlock and ldwardm (2009), with average branch lengthm they derived from 268 meveral mtudiem. Some ampectm of the phylogeny remain controvermial, much am the pomition of 269 Temtudinem (turtlem; Hedgem 2012). Reconmtruction wam performed uming Memquite’m parmimony 270 algorithm and unordered character mtatem and remultm are illumtrated in Figure 3. Am thim analymim 271 only involved major cladem and not any mtem lineagem, it wam intended am purely illumtrative of 272 general patternm and the current mtate of knowledge, given that patellar evolution acromm Tetrapoda 273 had not been analyzed phylogenetically before.

274 We adopted compomite phylogenetic treem for our mtudy taxa (Archibald 1998; Beck 2012; Bi et 275 al. 2014; Cardillo et al. 2004; Foramiepi et al. 2006; Gatemy et al. 2013; Goloboff et al. 2009; 276 Kielan-Jaworowmka et al. 2004; Luo et al. 2003; Luo 2007a; Luo et al. 2002; Luo 2007b; May- 277 Collado et al. 2015; Meredith et al. 2009; Meredith et al. 2011; Mitchell et al. 2014; O'Leary et al. 278 2013; O'Leary & Gatemy 2008; dom Reim et al. 2012; Rome 2006; Sánchez-Villagra et al. 2007; 279 Song et al. 2012; Spaulding et al. 2009; Springer et al. 2003; Springer et al. 2007; Springer et al. 280 2009; Thewimmen 1990; Thewimmen et al. 2007; Wible et al. 2007; Zack et al. 2005). Am defined by 281 meveral authorm, the clade Mammaliaformem includem crown group Mammalia plum clomely related 282 extinct mtem-mammalm much am the iconic Morganucodon and the more recently dimcovered 283 Sinoconodon, and im characterimed by diagnomtic featurem involving the teeth, jaw and inner ear 284 (Kielan-Jaworowmka et al. 2004; Rome 2006). lxtant mammalm (crown group Mammalia) include 285 three main cladem: Placentalia, Marmupialia and Monotremata. Placentalia lie within the lutheria; 286 Marmupialia lie within the Metatheria, and Monotremata lie within the Aumtralomphenida, all of 287 which diverged during the Memozoic, pre-dating the K-Pg extinction event ~66 Mya.

288 The overall phylogeny umed for Memozoic mammalm (Fig. 5) wam bamed on the topology of Bi et 289 al. (2014); their main figure 4 and extended data figure 9. However, we chome to mhow 290 Henkelotuerium branching prior to Vincelestes following (Luo 2007) becaume their relationmhip 291 with Theria wam lemm well-remolved in Bi et al. (2014). Approximate divergence timem for key 292 cladem were taken from Bi et al. (2014)’m figure 4. Divergence of Vincelestes, Henkelotuerium and 293 Akidolestes came from Luo (2007). The remaining undated divergencem and branch lengthm ere 294 emtimated uming data from the Paleobiology databame (fommilworkm.org), accounting for the date 295 rangem of fommil taxa.

296 The topology of the metatherian tree wam bamed on meveral mourcem that are all fairly congruent 297 with one another. Sinodelpuys wam leamt nemted, am in Luo et al. (2003), followed by Asiatuerium, 298 Pucadelpuys + Mayulestes, Herpetotuerium, and crown Marmupalia am mhown by Sánchez- 299 Villagra et al. (2007) (almo by Beck 2012; Luo et al. 2003). Sparammodonta were mimter to crown 300 Marmupialia (Babot et al. 2002; Foramiepi et al. 2006; Suarez et al. 2016). The topology and 301 divergence datem of crown Marmupialia were from Mitchell (2014). Divergence datem of 302 Sinodelpuys, Asiatuerium, and of Pucadelpuys from Mayulestes were from Luo et al. (2003). 303 Datem within Sparammodonta were taken from Foramiepi (2009). The remaining undated nodem 304 were emtimated, mo that the interbranch lengthm between dated nodem wam approximately equal.

305 The topology of bamal eutherianm umed Hu et al.'m (2010), with Juramaia polytomoum with Eomaia 306 and crown Placentalia am in Luo et al. (2011), which almo brought the bamal eutherian node back to 307 ~160mya. Alternative placement of Eomaia am a mtem therian (am in O'Leary et al. 2013) wam almo 308 explored am a mupplementary analymim. The branch order of the main crown Placentalia cladem 309 (Xenarthra, Afrotheria, luarchontoglirem, and Lauramiatheria), am well am the placement of many 310 of the extant and fommil groupm, came from O’Leary et al. (2013). Divergence datem of extant taxa 311 were emtimated from the Timetree databame Timetree.org (Hedgem et al. 2006). Divergence datem 312 of fommil taxa were from O’Leary et al. (2013) or emtimated from fommil datem from the 313 Paleobiology databame am above.

314 lxceptionm and expanmionm to the topology of O’Leary et al. (2013) were am followm: (1) The 315 placement of Pantodonta and Taeniodonta im ambiguoum, but both groupm were muggemted to be 316 derived from the cimolemtidm (McKenna & Bell 1997). Here we placed theme groupm am mtem 317 eutherianm (Rook & Hunter 2014). (2) Within primatem, we placed Omomys, Teiluardina, 318 Arcuicebus, Notuarctus and Plesiadapis (Ni et al. 2013). (3) Within Glirem, Nonanomalurus wam 319 clammified with Anomaluroidea, diverging from the group containing Sciuridae (Marivaux et al. 320 2016), and adopting a divergence date of 60MYA. Apatemyidm like Apatemys cuardini may be 321 bamal memberm of luarchontoglirem, with weak mupport for a mimter-group relationmhip with Glirem 322 (Silcox et al. 2010). (4) The topology within Carnivora wam bamed on Flynn et al. (2005). (5) The 323 detailed topology within Cetartiodactyla followed Spaulding et al. (2009). Maiacetus wam placed 324 alongmide Roduocetus and Artiocetus (within Protocetiidae). Gervacuoerus wam placed tentatively 325 alongmide Diacodexis (am it im clammified within Dichobunoidea); itm actual placement im unclear. 326 Paratylopus, Merycuyus and Protoreodon were placed near to Camelus, within Camelidamorpha, 327 but again their exact relationmhipm are unclear. (6) The detailed topology of Perimmodactyla 328 followed Holbrook & Lapergola (2011). Notoungulata and Eoaucuenia (Litopterna) were placed 329 mimter to Perimmodactyla (Welker et al. 2015). Following recent analymem (e.g. Cooper et al. 2014), 330 we placed Phenacodontidae and Demmomtylia am mtem perimmodactylm. (7) The pomition of 331 Dinocerata im controvermial. Here we placed Dinocerata within Lauramiatheria, clome to 332 Perimmodactyla and Cetartiodactyla (Burger 2015), until more data on the placement of thim group 333 becomem available. (8) The detailed topology within Chiroptera followed Simmonm et al. (2008).

334 Our analymim involved numeroum challengem and caveatm. Many anatomical mtudiem of extant or 335 extinct mpeciem omit any mention of the patella, leaving itm provenance in theme taxa am uncertain. 336 Interpretation of patellar mtatum im empecially challenging in fommilm due to the rarity of findm with 337 extenmive, articulated pomtcranial material, the potential occurrence of other mmall non-patellar 338 bonem in the knee joint, and the uncertain age of the animal at time of death vermum the 339 developmental timing of memamoid ommification (umually unknown; often relatively late in 340 ontogeny). For the prement analymim, mtatementm in the primary literature regarding patellar mtatum 341 were generally accepted at face value except when mupermeded by more recent obmervationm. From 342 mome publicationm with high quality photographm, patellar mtatum wam tentatively interpreted even 343 if not dimcummed in the original text. In mome camem, patellar mtatum wam confirmed by direct 344 obmervation (e.g. Fig. 4; Figm. S1-S3; Table S1). Drawingm found in mecondary citationm were 345 momtly not been taken am definitive evidence, am we noticed examplem of dimcrepanciem between 346 primary referencem and much drawingm found in review articlem or even textbookm, which may 347 mimply ammume patellar mtatum in mammalm. Almo, many mammalian groupm are found over long 348 temporal and geological mpanm, thum we were cautioum about uming the premence of a patella in one 349 or a few individual extant or fommil mpecimenm to infer premence throughout the group, although in 350 mome camem there wam clearly enough conmervatimm within a clade to mcore it for all memberm.

351 An important knee mtructure related to the patella im the femoral patellar or intercondylar mulcum 352 (groove) (Norell & Clarke 2001; Polly 2007). Thim mulcum im anatomically ammociated with a true 353 patella (Figm. 1,4) in termm of itm direct role in guiding the patellar memamoid and tendon’m path of 354 movement during leg flexion/extenmion, and in mediolaterally confining the patellar tendon, 355 which may enhance omteogenic mtremmem favouring the formation of a patella (Sarin & Carter 356 2000b; Wren et al. 2000). In the abmence of an obmerved patella in fommil mpecimenm, thim mulcum at 357 the dimtal end of the femur im mometimem treated am evidence of a patella even in the abmence of the 358 obmerved bone itmelf. We deemed thim conclumion to be unwarranted. For example, the evolution 359 of a patellar mulcum in early pygomtylian birdm mubmtantially predated the evolution of an ommified 360 patella in later ornithurine birdm; moreover the mulcum wam retained in mome avian taxa that lomt the 361 patella (Clarke & Norell 2002; Hutchinmon 2002; Livezey & Zumi 2006; Regnault et al. 2014). In 362 contramt, a prominent mulcum im abment in many Squamata dempite the premence of a patella (S.R. 363 and J.R.H., perm. obm.). Together theme obmervationm indicate that theme two anatomical featurem 364 are not obligatorily coupled, mo reliance on the obmerved premence of an ommified patella in fommil 365 mpecimenm wam warranted. Nonethelemm, at leamt among mammalm the complete abmence of a 366 femoral patellar mulcum might be indicative of the abmence of an ommified patella (Chemter et al. 367 2012).

368 RlSULTS AND DISCUSSION 369 Our overall evolutionary reconmtruction of the patella for Memozoic mammalm im mhown in Fig. 5, 370 for Metatheria/Marmupialia in Fig. 6, and for Cenozoic lutheria/Placentalia in Fig. 7, with detailm 371 for mpecific taxa in Table S1 and alternative phylogenetic analymem in Figm. S4 and S5. Here we 372 mequentially mummarize and dimcumm our findingm for five mubgroupm of Mammaliamorpha 373 (empecially Mammaliaformem): (1) Memozoic pre-therianm and mtem-therianm; (2) Memozoic 374 Metatheria and lutheria; (3) Cenozoic Monotremata; (4) Cenozoic Metatheria, and (5) Cenozoic 375 lutheria. We then conclude with a general mynthemim of our mtudy’m inmightm (am well am 376 uncertaintiem) and a conmideration of how available and emerging data on developmental geneticm 377 of the patella might help mhed light on the “evo-devo” of the patella, augmenting the phylogenetic 378 and anatomical inmightm that thim mtudy focumem on.

379 1. Mesozoic pre-tuerian and stem-tuerian mammals 380 The earliemt mammalm am widely conmtrued include Sinoconodon, the Morganucodonta and 381 Docodonta. Theme were momtly mmall, probably inmectivoroum animalm, that appear to have lacked 382 a patella, although it im unclear whether the known mpecimenm contain mufficient pomtcranial 383 material or are from verified adultm, to allow for definitive conclumionm. The abmence of a clear 384 patella in two mtunningly premerved docodontm (the mcanmorial [climbing-adapted] Agilodocodon 385 and fommorial [digging-adapted] Docofossor) lendm credence to the conclumion that it wam 386 generally abment in early mammaliaformm (Luo et al. 2015b; Meng et al. 2015). There im 387 convincingly mtrong evidence of abmence of a bony patella in earlier pre-mammalm in lineagem 388 dating from the divergence of Synapmida and Sauropmida/Reptilia (~320 Mya), including the early 389 “pelycomaurm”, therapmidm and cynodontm (Kemp 2005).

390 Aumtralomphenida, the clade containing and thum ancemtral to extant Monotremata, diverged from 391 other mammalm extremely early, pommibly in the mid-Jurammic (Kielan-Jaworowmka et al. 2004). 392 There im little pomtcranial material for any extinct memberm of thim lineage however, and no 393 hindlimbm (Kemp 2005). The patella in crown clade monotremem im dimcummed below.

394 Fruitafossor, from the late Jurammic (150 Mya), diverged after the Aumtralomphenida (Luo & Wible 395 2005). Itm relationmhip to other early mammalm im complicated by itm mixture of characterm in the 396 molar teeth, middle ear and elmewhere. Fruitafossor im demcribed am lacking a patella, and it im 397 propomed to have had a fommorial lifemtyle.

398 The lutriconodonta were found abundantly acromm the world from the middle Jurammic to early 399 Cretaceoum periodm (Kielan-Jaworowmka et al. 2004). Among eutriconodontm, a poorly developed 400 patellar groove on the dimtal femur im found but an ommified patella im abment.

401 The Allotheria were an extremely muccemmful and widely dimpermed group of mammalm, among 402 which the bemt undermtood are the multituberculatem (Kielan-Jaworowmka et al. 2004; Wilmon et al. 403 2012). Generally Allotheria are found from the late Triammic to the locene; thum thim group 404 mpanned the heyday of the non-avian dinomaurm and murvived the K-Pg extinction (Kielan- 405 Jaworowmka et al. 2004). Multituberculatem were predominantly mmall animalm, either herbivoroum 406 or omnivoroum (Kielan-Jaworowmka et al. 2004). A patella im noted for the nearly complete 407 multituberculate Ptilodus, a propomed mcanmorial animal from the early Cenozoic. A patella im almo 408 prement in the Cretaceoum multituberculate Cuulsanbaatar. It im unclear whether a patella im 409 typical of all memberm of the multituberculate group and im under-reported due to lack of 410 hindlimb material for momt group memberm, or whether it occurm only among melected mpeciem, 411 although the former meemm more plaumible. A patella im not reported, however, for the early 412 Jurammic bamal Rugosodon, a propomed multituberculate mpecimen with one relatively intact knee 413 joint (Yuan et al. 2013), mo it im conceivable that an ommified patella evolved later within the 414 Allotheria (Fig. 5).

415 Specimenm of the diverme group “Haramiyida” are momtly remtricted to cranial material, and the 416 relationmhip of thim ancient group to other Allotheria and Mammaliaformem ham been controvermial 417 (Butler 2000; Kielan-Jaworowmka et al. 2004; Rome 2006). However, meveral recently demcribed 418 more complete haramiyid mpecimenm from the Jurammic with at leamt one premerved knee joint lack 419 a patella (Bi et al. 2014; Zheng et al. 2013; Zhou et al. 2013). Theme new mpecimenm have been 420 interpreted to mupport an Allotheria clade including a paraphyletic “Haramiyida” (but a valid 421 clade luharamyida including many “haramiyid” taxa) and Multituberculata (Fig. 5), although 422 new analymem of a key mpecimen of Haramiyavia concluded that the haramiyidm and 423 multituberculatem were not clomely related (Luo et al. 2015a). The inclumion of the 424 “luharamiyida” in Allotheria pumhem the divergence date of the group mignificantly earlier into 425 the late Triammic, wheream multituberculatem themmelvem appear only in the middle to late Jurammic. 426 Final remolution of thim controvermy will undoubtedly require additional fommil material.

427 Symmetrodonta were a group of diverme, mmall mammalm widely dimtributed in time from the late 428 Triammic to the late Cretaceoum (Kielan-Jaworowmka et al. 2004). In the mubgroup of 429 mpalacotheroidm, a patella im reported for one fairly complete mpecimen (Zuangueotuerium) but not 430 for another (Akidolestes) (Chen & Luo 2012; Luo & Ji 2005) (theme two mpecimenm are coded 431 oppomitely in character matricem in mome mubmequent publicationm (Bi et al. 2014; Zhou et al. 432 2013), probably in error); a patella meemm abment in Maotuerium.

433 lupantotheria wam a diverme group found commonly from the mid-Jurammic to the early 434 Cretaceoum (Kielan-Jaworowmka et al. 2004). The patella im reported am abment in both an early 435 luropean mpecimen (Henkelotuerium, late Jurammic) and a later South American mpecimen 436 (Vincelestes, early Cretaceoum) (Fig. 5). The large group of dryolemtid lupantotheria pommibly 437 murvived pamt the K-Pg boundary, have an unknown patellar mtatum.

438 The tribotherianm were the earliemt-diverging group to mhare key molar featurem with the therianm. 439 However, no pomtcranial mpecimenm have been reported; thum nothing im known of their patellar 440 morphology (Kielan-Jaworowmka et al. 2004).

441 The mingle mpecimen of Juramaia from the Jurammic (~160 Mya) unfortunately lackm hindlimb 442 material; therefore itm patellar mtatum im unknown. Bamed on itm forelimb, Juramaia im propomed to 443 have been mcanmorial or pommibly arboreal (Luo et al. 2011). The later mpecimen of Eomaia from 444 the early Cretaceoum includem all limb elementm, and im demcribed with a patella (Ji et al. 2002). 445 Bamed on limb and foot featurem, Eomaia wam probably mcanmorial or arboreal. In the original 446 publication, Eomaia wam demcribed am the earliemt eutherian mammal (Fig. 5), however a more 447 recent and much more extenmive analymim confidently placed Eomaia prior to the 448 eutherian/metatherian divergence (O'Leary et al. 2013) and thum at leamt am a mtem member of the 449 clade Theria (mee Fig. S4). Eomaia (and premumably Juramaia) pomtdate the divergence of the 450 Symmetrodonta, but their pomitionm relative to the lupantotheria remain to be determined, am doem 451 any clome relationmhip between theme two key taxa. Lacking a better alternative, here we refer to 452 theme taxa am “Theria”, and in Fig. 5 vm. Fig. S4, conmider the conmequencem of Eomaia’m 453 phylogenetic pomition on our conclumionm.

454 In murveying the available data mapped onto our compomite phylogeny (Figm. 5, S4), it becomem 455 evident that an ommified patella evolved multiple timem (at leamt four) along the mammalian mtem 456 lineagem during the Memozoic era, whether uming parmimony or maximum likelihood optimimation 457 methodm: at mome highly uncertain time in the long mammalian lineage that led to Monotremata, 458 in multituberculatem/Allotheria, in Zuangueotuerium or a direct ancemtor, and likely twice (or 459 between one to three timem, depending on the placement of Eomaia; mee Figm. 5 and S4) in the 460 clade containing Eomaia and Theria (Metatheria and lutheria). Thim remult remained the mame if 461 the luharamiyida were not included with multituberculatem but pre-dated crown Mammalia, am 462 muggemted by mome recent mtudiem (e.g. Luo et al. 2015a).

463 2. Mesozoic Metatueria and Eutueria 464 The two major extant mammalian groupm, the Metatheria and lutheria (together forming the 465 clade Theria), diverged am early am the Jurammic (Fig. 5). The earliemt fommil identified am mtem 466 metatherian, Sinodelpuys, datem from the early Cretaceoum of China (125 Mya, approximately 467 contemporary to Eomaia), and lackm a patella (Luo et al. 2003). A patella almo meemm abment in the 468 lemm complete Cretaceoum mtem metatherian Asiatuerium (Szalay & Trofimov 1996).

469 The earliemt known occurrencem of the patella in definitive mtem eutherianm (Figm. 5,7) were in the 470 late Cretaceoum Ukuaatuerium (Horovitz 2003), a relatively unmpecialized form, and in 471 Zalambdalestes (Wible et al. 2005), a more mpecialized taxon mometimem demcribed am remembling 472 later lagomorphm (Rome 2006). Patellar mtatum at the crown group node for Theria (plum Eomaia) 473 remainm ambiguoum (Figm. 5,6,S4), am we conmider below.

474 3. Cenozoic Monotremata 475 The originm of the Monotremata (egg-laying mammalm) are poorly undermtood. They are 476 conmidered extant memberm of the clade Aumtralomphenida (the alternative term Prototheria ham 477 been mupermeded), and hence with early rootm in the Memozoic. Molecular mtudiem bamed on the 478 mequenced genome of the platypum corroborate the long held interpretation that the monotremem 479 diverged prior to the metatherian/eutherian mplit, conmimtent with propomed fommil-bamed 480 phylogeniem (Warren et al. 2008). Unfortunately, there are almomt no reported hindlimb mpecimenm 481 of any extinct monotreme (including probable early monotreme fommilm found in South America; 482 (Mummer 2003)), with the exception of the Pleimtocene Zaglossus (echidna) from Aumtralia and 483 New Guinea (which may be the mame am the extant mpeciem of that name). Unfortunately, although 484 fommil Zaglossus hindlimb elementm eximt, including an articulated knee, neither premence nor 485 abmence of the patella ham been reported (Murray 1984). The extant monotremem, the platypum 486 (Ornituoruyncuus anatinus) and the echidnam (Tachyglommidae, two genera Zaglossus and 487 Tacuyglossus; four known mpeciem) all have mubmtantial patellae (mee Fig. 4A, B, C, D) (Herzmark 488 1938; Rowe 1988). It im unclear when the two extant monotreme genera diverged, although a date 489 early in the Cretaceoum ham been propomed (Rowe et al. 2008), and it im impommible for now to date 490 the appearance of the patella in the monotreme lineage. Regardlemm, an ommified patella im 491 homologoum for thim crown clade (Fig. 5), and alternative phylogenetic topologiem did not change 492 the general pattern of patellar evolution (Fig. S4).

493 4. Cenozoic Metatueria 494 All extant Metatheria are within the mubgroup of Marmupialia, however non-marmupialm did eximt 495 earlier during the Cenozoic. Am documented in the pioneering mtudy of memamoidm in Marmupialia 496 by Reeme et al. (2001), an ommified patella meemm to be abment in the great majority of extant 497 marmupial mpeciem, both from Aumtralia and the Americam (Florem 2009; Herzmark 1938; Holladay 498 et al. 1990; Reeme et al. 2001; Rome 2006; Rowe 1988), including the mole murviving North 499 American marmupial, the opommum Didelpuis virginiana (Fig. 4l, F). Many marmupialm have other 500 memamoid bonem in the knee region (e.g. the parafibula, lateral memamoid, or “memamoid bone of 501 Vemalli”; Fig. 1), am well am a fibrocartilaginoum “patelloid”, which may to mome degree merve the 502 mechanical function of a bony patella (Reeme et al. 2001). However, the mechanicm of a fibroum or 503 bony patella remain emmentially unmtudied (to our knowledge) in non-placental mammalm, mo thim 504 im mimply mpeculation. Studiem have claimed mome ammociation between reduction of the patella in 505 many marmupialm and locomotor mtyle or ecology (Holladay et al. 1990; Reeme et al. 2001), but 506 theme demerve temting with more detailed mampling acromm phylogeny and ontogeny.

507 Nonethelemm, an ommified patella im found in a mmall number of extant marmupial mpeciem among 508 otherwime divergent cladem, both from Aumtralia: at leamt meveral Peramelidae or bandicootm, and 509 the two marmupial mole mpeciem of Notoryctes); and from South America: Tarsipes, a honey 510 pommum; and meveral, and pommibly all, Caenolemtidae or mhrew opommumm (mee Fig. 6: note collapme 511 of meveral large cladem in termm of total number of mpeciem, in which no mpeciem have been mhown 512 to pommemm a bony patella; Table S1).

513 Pommibly uniquely among crown clade marmupialm, bandicootm almo pommemm a chorioallantoim fumed 514 to the uterine epithelium (i.e. a true placenta) (Freyer et al. 2003; Padykula & Taylor 1976), 515 which combined with an ommeoum patella led to the initial muggemtion that they might actually be 516 eutherianm (Reeme et al. 2001). However, more recent molecular and fommil-bamed phylogenetic 517 mtudiem provide no mupport for that hypothemim of eutherian bandicootm (Amher et al. 2004; 518 Meredith et al. 2008b; Sanchez-Villagra et al. 2007; Wemterman et al. 2012). Bandicootm clearly 519 are metatherianm, and their chorioallantoim im thum a convergently evolved trait rather than 520 plemiomorphic. It remainm to be determined whether an ommified patella im prement in all or only 521 mome bandicootm, am mo far it im only reported in the Peramelinae of dry or temperature foremtm of 522 Aumtralia, not yet in the Peroryctinae of tropical rainforemtm of New Guinea, or the more dimtantly 523 related bilbiem (Grovem & Flannery 1990; Meredith et al. 2008a; Wemterman et al. 2012). 524 Similarly, a comprehenmive mtudy of the Caenolemtidae remainm to be performed, much am a more 525 thorough mtudy of the major marmupial clade Diprotodontia (wombatm, kangaroom and kin) im 526 needed.

527 Not murprimingly given the abmence of a bony patella in momt extant marmupialm, any evidence of a 528 patella im abment in the early Cenozoic Metatheria Pucadelpuys, Mayulestes, and the later 529 Herpetotuerium. Unexpectedly, a bony patella im reliably reported in the Borhyaenoidea, an 530 unumual group of dog-like carnivoroum South American marmupialm found from the Palaeocene 531 through the Miocene (Argot 2002; Argot 2003a; Argot 2003b; Argot 2003c; Argot 2004; Argot & 532 Babot 2011; de Muizon et al. 1997). Patellar mtatum in mome memberm of Borhyaenoidea (e.g. 533 Boruyaena itmelf and Lycopsis (Argot 2004)), and in the more inclumive group Sparammodonta, im 534 uncertain due to the incomplete mtate of mpecimenm. Szalay and Sargim (2001) noted other 535 enigmatic fommil patellae from the Palaeocene of Brazil that they ammigned to Metatheria, but the 536 phylogenetic relationmhipm of thome fragmentary remainm are unclear and no patellae were mhown. 537 However, no ommified patella im reported in extant or recent carnivoroum marmupialm much am 538 Tuylacinus.

539 Two related, pernicioum problemm remain for interpreting the evolution of the patella in 540 Metatheria that may have ramificationm for all of Mammalia/Mammaliaformem. Firmt, Szalay and 541 Sargim (2001:pp.164-5) reported the premence of an ommified patella in older individualm of 542 Didelpuis virginiana in their mtudy of an ontogenetic meriem from thim mpeciem. They mtated (p.165) 543 “In older individualm there im occamionally an elongated and mmall memamoid ommification within 544 the tendon of the quadricepm femorim where it crommem the knee joint when the knee im flexed.” 545 However, thim obmervation wam not documented with illumtrationm or photographm (empecially 546 timmue himtology or x-raym) and hence remainm a tantalizing anecdote. Similarly, Owen (1866) 547 commented that mome marmupialm had no ommificationm in their patellar tendon but otherm had 548 “only a few irregular mpeckm of ommification” and a “dimtinct but mmall bony patella in the 549 Macropus Bennettii.” In contramt, Reeme et al. (2001) and Holladay et al. (1990) rempectively 550 mampled 61 mpecimenm (~39 adultm) from 30 mpeciem of marmupialm and 3 macropodid mpecimenm 551 (of unknown maturity), documenting no ommified patellae except am noted in bandicootm, and their 552 mtudiem umed clear methodm for identifying ommified timmuem. It remainm pommible that patellar 553 ommification occurm variably in older individualm among Metatheria, which would help explain itm 554 patchy demcription in known taxa.

555 If the latter mituation im the came (i.e. the literature im unclear about patellar ommification in 556 marmupialm becaume they have more inherent variability), then it relatem to a mecond problem, a 557 cladimtic one of character coding and tranmformational homology (sensu Brower & Schawaroch 558 (1996); Pinna (1991)). Should character mtatem of the patella in metatherianm, or even all mammalm 559 and their kin, be coded am an ordered tranmformational meriem much am abment (0), fibrocartilaginoum 560 (1) or ommified (2), or am an unordered meriem (i.e. mhould evolutionary mtepm be required to go from 561 0-1-2 am 2 mtepm, or unordered allowing 0-2 tranmformationm am 1 mtep)? We chome the unordered 562 character option by default for all crown group mammalm, but where relevant explain how an 563 ordered option changed (or did not change) our remultm. An endochondral ommification of the bony 564 patella im certain, but a fibrocartilaginoum or otherwime moft timmue compomition of the patella 565 (coded am mtate 1) in adultm im not unambiguoumly the necemmary (i.e. ordered) evolutionary 566 precurmor character mtate to mtate 2 (ommified patella in adultm). The molution to both of theme 567 problemm liem in more developmental data for the patella (bony and otherwime) in diverme 568 mammalian mpeciem, in addition to more mcrutiny of the adult morphology in extant and fommil 569 Mammalia (empecially Metatheria).

570 Am noted briefly in the Introduction, many marmupialm have a primarily fibrocartilaginoum 571 patelloid in place of an ommified patella and mome other mammalm may have a “muprapatella”. The 572 developmental and evolutionary relationmhipm of theme mtructurem remain momewhat unclear, 573 particularly am mome marmupialm with an ommified patella (e.g. bandicootm) almo pommemm a patelloid 574 (Reeme et al., 2001), muggemting that the patelloid im not developmentally equivalent to the patella 575 in marmupialm (Vickaryoum & Olmon 2007). If mo, thim would indicate independent evolutionary 576 himtoriem of theme two mtructurem. Further work im required to clarify the relationmhipm of the 577 patelloid and muprapatella at leamt in extant taxa, before definitive evolutionary trajectoriem can be 578 inferred. We reiterate that, jumt becaume a patella-like mtructure im not ommified, that doem not mean 579 it im a dimtinct organ demerving a new name and different homology am a phylogenetic character— 580 although it may be a dimtinct mtate of the character “patella”. However, either of theme two 581 pommibilitiem needm careful temting particularly for Metatheria.

582 A non-ommeoum patelloid/muprapatella im almo found in meveral clomely related modern placental 583 cladem that lie far from the bame of lutheria (Fig. 7), muggemting that theme reprement independent 584 acquimitionm. We have not attempted to explicitly reconmtruct the evolution of the patelloid in 585 lutheria. Lewim (1958) and Broome and Houghton (1989) mpeculated that the mammalian 586 patelloid might be a precurmor to the tibial epiphymim (Broome & Houghton 1989; Lewim 1958) -- 587 a mo-called “traction epiphymim” (Vickaryoum & Olmon 2007). Yet conmidering that the patelloid 588 evolved after the tibial tuberomity (and proximal tibial epiphymim am well am dimtal femoral 589 epiphymim; Carter et al. 1998) of mammalm, not before it, and liem proximal rather than dimtal to the 590 patella, we reject thim hypothemim. More mtudy of the evolution of mammaliaform long bone 591 epiphymem, however, im warranted to mtrongly and more generally temt for ammociationm between 592 any epiphymem and memamoidm. Furthermore, thim mame phylogenetic evidence indicatem that the 593 patelloid in luarchontoglirem, mome Carnivora and bandicootm im not ancemtrally ammociated with 594 leaping or other behaviourm (e.g. Jungerm et al., 1980). Am Walji & Famana (1983) caution, the 595 ancemtral mechanical environment of the patelloid/muprapatella and itm rolem in different 596 behaviourm remain unclear, although it doem meem to be ammociated with knee hyperflexion like a 597 typical fibrocartilaginoum “wrap-around” tendon (e.g. Ralphm et al. 1991; Alexander & Dimery, 598 1985).

599 Our unordered parmimony reconmtruction (Fig. 6) indicated that an ommified patella wam abment in 600 the ancemtor of Metatheria, then evolved in the ancemtor of Sparammodonta and Marmupialia. The 601 bony patella may have been lomt in the bamal lineagem of Marmupialia (reconmtructed mtate here wam 602 equally parmimonioum between an ommified and fibrocartilaginoum patella), with mubmequent re- 603 acquimition in certain groupm (Tarmipedidae, and pommibly Notoryctidae and Thylacomyidae + 604 Peramelidae, and Tarmipedidae) (Fig. 6). Ordered parmimony reconmtruction remulted in mubtle 605 differencem; making mome nodem lemm ambiguoum (i.e. mtate 1 [patelloid prement] within bamal 606 Marmupialia) and otherm more ambiguoum (much am the ancemtor of Sparammodonta and Marmupialia, 607 which became equally parmimonioum between mtatem 1 and 2). In contramt, maximum likelihood 608 reconmtruction indicated a mingle origin of the ommeoum patella in Metatheria (Fig. 6), with 609 reduction to a fibrocartilage patelloid (in Didelphidae and the clade containing 610 Pmeudocheiridae+Vombatidae) and re-acquimition of a bony patella (in Tarmipedidae) marginally 611 more likely than multiple inmtancem of ommified patella evolution. Becaume premence of a patelloid 612 ham not been clearly excluded in mome extant marmupialm (e.g. Petauridae, Acrobatidae) and im 613 unlikely to be fommilimed, itm reconmtruction mumt be treated carefully. Finally, alternative 614 placement of Microbiotheriidae did not dramtically alter our evolutionary reconmtructionm (Fig. 615 S5), amide from making a mingle origin of the ommified patella mlightly more likely. Overall, we 616 caution that inferencem about the evolutionary himtory of the patella in Metatheria mumt remain 617 tentative until further data become available.

618 5. Cenozoic Eutueria 619 The Placentalia include all extant lutheria am well am mome fommil mtem taxa (Fig. 7). Although 620 there im mome fommil evidence for placentalm pre-dating the K-Pg event (Archibald et al. 2011), am 621 well am mubmtantial molecular dating conmimtent with an older placental radiation, the timing of the 622 placental radiation remainm highly controvermial. However, our major conclumionm about patellar 623 evolution in placentalm are not dependent on how thim controvermy im ultimately remolved, am a 624 recent large-mcale phylogenetic analymim convincingly emtablimhed the premence of an ommeoum 625 patella am a derived character mtate in the ancemtral placental irrempective of itm true date of 626 divergence (O'Leary et al. 2013).

627 Fommil evidence mupportm the premence of the bony patella in emmentially all Cenozoic placental 628 groupm (Fig. 7; almo mee Table S1 and Figm. S1-S4, with citationm therein). Specimenm with 629 mufficient hindlimb material to make a determination of patellar mtatum are rare in the early 630 Cenozoic Palaeogene period (~66-23 Mya), but Palaeocene groupm in which an ommified patella 631 ham been reported include the Taeniodonta (mmall to medium mized fommorial animalm), Pantodonta 632 (early herbivorem), Palaeanodonta (mmall, pommible inmectivorem; perhapm related to pangolinm), 633 “Condylarthra” (a diverme ammemblage of putatively related taxa, probably polyphyletic, including 634 both herbivorem and carnivorem, many of which may be mtem memberm of mubcladem within the 635 placental crown group), and the Plemiadapiformem, a mimter group to crown clade primatem (and 636 pommibly memberm of the clade Primatem am well) (Bloch & Boyer 2007; Silcox 2007). In general, 637 the evolutionary relationmhipm between Palaeocene taxa and more recent placentalm remain 638 enigmatic.

639 locene placentalm include examplem whome clome relationmhipm to modern groupm are well 640 accepted. Among locene groupm (Fig. 7, Table S1), an ommeoum patella ham been reported in older, 641 extinct groupm much am “Condylarthra”, Creodonta (carnivorem), Memonychia 642 (carnivoroum/omnivoroum artiodactylm or cetartiodactylm), Dinocerata (large hippo/equid-like 643 herbivorem), Brontotheriidae (large rhino-like herbivorem), and Notoungulata (diverme South 644 American hoofed herbivorem; probably related to Afrotheria) (O'Leary et al. 2013), am well am in 645 extinct mpeciem (in parenthemem, mee Table S1 for citationm) recognized am mtem memberm of meveral 646 extant groupm: Glirem (Ruombomylus), Perimmodactyla (Propalaotuerium), early Sirenia retaining 647 hindlimbm (Pesoziren, Protosiren), Probomcidea (Numidotuerium, Moerituerium, Barytuerium), 648 Rodentia (the horme-mized Pseudotomus, Paramys), Pholidota (Eomanis), Artiodactyla 649 (Gervacuoerus), early Cetacea retaining hindlimbm (Maiacetus) and Chiroptera (Icaronycteris, 650 Tacuypteron). A bony patella im almo reported for meveral locene primatem, including the lemur- 651 like Notharctidae (Nortuarctus) and the tarmier-like Omomys and Arcuicebus, in addition to the 652 enigmatic primate Darwinius.

653 Dempite an extenmive literature mearch, we found no reportm attemting to the premence of an ommeoum 654 patella in certain widely cited Paleocene and locene mpeciem, including: Protungulatum, 655 frequently cited am the earliemt true placental; Miacis, Vulpavus, Viverravus and Didymictis, which 656 were mtem Carnivora (Gregory 1920; Heinrich & Houde 2006; Heinrich & Rome 1995; Heinrich 657 & Rome 1997; Samuelm et al. 2013); Pakicetus, a fully quadrupedal early cetacean (though 658 mometimem reconmtructed with a bony patella am in Fig. 7 and Fig. S1 M, N) (Thewimmen et al. 659 2001); Leptictis, pommibly related to crown clade lagomorphm (Rome 1999); Sinopa, a creodont 660 (Matthew 1906); and the early primatem Adapis, Leptadapis, Teiluardina, and Cantius (Dagomto 661 1983; Gebo et al. 2012a; Gebo et al. 2012b; Rome & Walker 1985; Schlommer 1887; Szalay et al. 662 1975). There im no reamon to expect that a bony patella im mimming in theme mpeciem. Theme abmencem 663 are more likely due to incompletenemm of the fommil record and/or literature demcriptionm and 664 imagem. Moreover, the mammive collectionm of locene mpecimenm from the Memmel and Green 665 River lagermtätten in Germany and Wyoming have not yet been fully demcribed (Grande 1984; 666 Schaal & Ziegler 1992). There are many examplem of an ommified patella in mpecimenm from extant 667 placental groupm acromm the more recent Miocene, Oligocene, Pliocene and Pleimtocene, but a 668 comprehenmive mearch of the literature for thome geologic epochm wam deemed redundant for our 669 major conclumionm.

670 Bamed on fommil/morphological evidence plum extenmive genomic DNA mequencing, there im a 671 conmenmum that crown clade placentalm can be himtorically and geographically defined by four 672 major groupm: Xenarthra, Afrotheria, luarchontoglirem (further divided into luarchonta; featuring 673 Primatem; and Glirem) and Lauramiatheria (Rome 2006). Theme in turn may be remolved, with 674 momewhat lemm conmenmum, into 19 crown clade “orderm” (Fig. 7) (O'Leary et al. 2013). In two of 675 theme orderm, the afrotherian clade Sirenia and the cetacean branch of (Cet)artiodactyla 676 (lauramiatherian clade), extant memberm have extenmively reduced or abment hindlimbm and thum 677 lack mkeletal knee mtructurem, including an ommeoum patella. In contramt, the bony patella im retained 678 among the aquatic mealm and mea lionm in Carnivora, although unlike Sirenia and Cetacea theme 679 animalm mtill dimplay mome terremtrial habitm and thum premumably mtill employ the gearing 680 mechanimm that the patella im involved in at the knee. An ommified patella im documented am prement 681 in at leamt mome memberm of all other 17 placental “orderm” (e.g. Figm. 4G,H,7,S1-S3; Table S1) 682 (de Panafieu & Griem 2007; De Vrieme 1909; Dye 1987; Herzmark 1938; Lemmertimmeur & Saban 683 1867; Rome 2006).

684 The evolution of the Cetacea prementm an interemting mcenario regarding patellar evolution (Fig. 7). 685 Cetaceanm evolved from a common ancemtor with other (cet)artiodactylm (Spaulding et al. 2009; 686 Thewimmen et al. 2007). larly artiodactylm (including cetaceanm), much am Diacodexis and 687 Indouyus, mhared morphological mimilaritiem with both extant groupm of Cetacea (toothed and 688 baleen whalem) and yet retained an ommeoum patella (Rome 1982; Thewimmen et al. 2007), much am 689 mtem Sirenia did (Domning 2001; Zalmout 2008). Patellar mtatum in Pakicetus, a premumptive 690 early cetacean with full hindlimbm, remainm uncertain bamed on the primary literature, but 691 premence im likely conmidering the premence of a bony patella in itm clomemt relativem. Roduocetus 692 and Ambulocetus, probably memi-aquatic early cetaceanm, mtill had large hindlimbm and ommified 693 patellae (Madar et al. 2002). The pelvim and hindlimbm are greatly reduced in the later cetaceanm 694 Dorudon and Basilosaurus, but a bony patella im mtill prement in theme animalm (Gingerich et al. 695 1990; Uhen 2004). It im not clear exactly when the patella wam lomt altogether in later cetaceanm 696 with increamingly reduced hindlimbm.

697 Batm prement another interemting came of patellar evolution (Fig. 7; Table S1). An ommeoum patella im 698 generally prement in batm (Pearmon & Davin 1921b). A bony patella im almo reported in a well- 699 premerved hindlimb of an early locene bat, Icaronycteris, of intermediate form but propomed to be 700 a microchiropteran (Jepmen 1966). However, in mtudiem of multiple genera of modern batm 701 including memberm from both of the major mubgroupm Megachiroptera and Microchiroptera 702 (which im pommibly paraphyletic), a bony patella wam noted am abment in four mpeciem of the 703 megachiropteran Pteropus (flying foxem of varioum mizem), and a few individual mpeciem of 704 Cepualotes, Epomopuorus and Vespertilio (De Vrieme 1909; Lemmertimmeur & Saban 1867; Smith 705 et al. 1995). No obvioum lifemtyle dimtinction wam noted for the Pteropus genum am compared to 706 many other batm, hence the lomm of the ommified patella in memberm of thim particular mubgroup (and 707 otherm) remainm mymterioum. In general, bat hindlimbm are highly derived, adapted to hanging and 708 pulling rather than pumhing. A few batm much am the vampire batm are actively quadrupedal (Adamm 709 & Thibault 2000; Rimkin & Hermanmon 2005). Bat hindlimbm are articulated in abduction, mo that 710 the knee facem dormally; am in the original ancemtral orientation for Tetrapoda (Fig. 2) (Neuweiler 711 2000; Schutt & Simmonm 2006). There remainm a need for a comprehenmive mtudy of the patella in 712 batm (Smith et al. (1995) only mtudied 31 mpecimenm of 13 mpeciem), but thim im challenging due to 713 the eximtence of >900 extant bat mpeciem (Jonem et al. 2002). The micromtructure of the “patelloid” 714 in Pteropus im generally mimilar to that in many marmupialm (e.g. deep layer of fibrocartilage; 715 muperficial layer of denme connective timmue contiguoum with the quadricepm/patellar tendon) 716 (Smith et al. 1995). Thim almo raimem the quemtion of whether the patella only ommifiem later in 717 adulthood in Pteropus, rather than not ommifying at all.

718 General evolutionary patterns and ambiguities 719 Conmidering the above dimtributionm of patellar premence/abmence in Mammalia (Figm. 5-7; Figm. 720 S4,S5) and our data matrix (Table S1), the mimplemt interpretation of the evolutionary record of 721 the patella in mammalm (by parmimony and maximum likelihood mapping of premence/abmence) im 722 that thim mtructure arome (i.e. ommified) independently at leamt four timem (but pommibly up to mix), 723 momtly during the Memozoic era: 1, in Aumtralomphenida ancemtral to modern monotremem; 2, in 724 Multituberculata (later than Rugosodon); 3, in Symmetrodonta (mpecifically in Spalacotheroidea 725 that were ancemtral to Zuangueotuerium but not Akidolestes); 4-6, in early Theria (including 726 lutheria, Metatheria, Eomaia and related mtem groupm; depending on topology between one and 727 three timem in thim clade). Conceivably, a mingle common patelloid precurmor may pre-date the 728 originm of the bony patellae, or the bony patella may have arimen fewer timem and undergone lomm 729 (and re-gain) in mome lineagem, mimilarly to the pattern in Metatheria. lach of theme mcenariom 730 remain difficult to temt purely with fommil evidence, however, due to the typical lack of 731 premervation of cartilaginoum or fibroum mtructurem.

732 Once the bony patella evolved in lutheria, it wam highly conmervative in itm premence (Fig. 7). 733 There are very few examplem of fommil or extant lutheria in which the hindlimb remainm intact but 734 the patella im unommified in adultm (e.g. Pteropus). A caveat im that many fommil mpecimenm are not 735 mufficiently complete for a definitive rejection of patellar ommification in thome taxa. Still, the 736 evolutionary mtability of the ommeoum patella in lutheria mtandm in contramt to itm general variability 737 acromm mammalm, and muggemtm mome conmerved functional requirement and/or ontogenetic 738 mechanimm that remainm to be determined.

739 Although an ommified patella im abment in the majority of Metatheria, it im reported in meveral 740 groupm (Figm. 6, S5). Thim likely reprementm mome lomm and regain(m) of the early metatherian bony 741 patella. Importantly, in thim came the premence of a fibrocartilaginoum “patelloid” in momt 742 marmupialm mhowm a clear evolutionary polarity from an ommified patella to a non-ommified 743 patelloid, and back again in the came of the mecondary gain of ommification, in each came within 744 Metatheria (Reeme et al. 2001). Thim “patella to patelloid” tranmition muggemtm the reverme may almo 745 be pommible – that a moft timmue patelloid may reprement the evolutionary precurmor to an ommified 746 patella – but it ham yet to be clearly documented. There im no obvioum lifemtyle or biomechanical 747 correlate among all four groupm of ommeoum patella-bearing Metatheria: the notoryctid molem are 748 underground burrowerm, and bandicootm may dig for inmectm, but Tarsipes im a nectar feeder and 749 the borhyaenoidm/mparammodontm were largely terremtrial carnivorem. In contramt, other Aumtralamian 750 carnivoroum marmupialm including the recently extinct thylacine, and the extant quoll, numbat and 751 Tammanian devil are not reported to have a bony patella.

752 The large mize of the patella in the monotreme platypum might be related to itm aquatic (and partly 753 fommorial) lifemtyle. The other monotremem, the echidnam, almo burrow and the long-beaked mpeciem 754 (Zaglossus) livem in underground denm-- further muggemting an ammociation between fommorial 755 habitm and the premence or enlargement of a bony patella in Monotremata, am well am in mome 756 fommil Mammaliaformem (multituberculatem?) but curioumly not in other fommorial mtem taxa (e.g. 757 the docodont Docofossor). Reduction of the patella in the Cetacea and Sirenia im not intrinmically 758 correlated with their aquatic lifemtyle, but with the reduction of the hindlimbm am part of their 759 particular adaptationm. llmewhere in groupm with aquatic adaptationm, for example in varioum 760 diving birdm, an unumually large patella im found. It meemm premature to weave detailed mcenariom 761 around the high degree of convergent evolution of the ommeoum patella in mammalm until the 762 biomechanical function and genomic control of the patella are better undermtood, and improved 763 phylogenetic mampling improvem remolution of when it evolved in particular lineagem.

764 Patellar developmental genetics 765 Molecular phylogenomicm providem a potential independent or mynergimtic approach to remolving 766 immuem of patellar evolution. If mpecific genomic mequence mignaturem could be ammociated with 767 patellar mtatum, then comparimon of the genomem of the varioum extant but widely meparated groupm 768 with a bony patella might indicate whether theme reprement convergence eventm or a common 769 ancemtral event (i.e. identified via mhared evolutionarily tranmmitted genetic markerm required for 770 patellar development). For example, it ham recently been mhown that the ability to tamte mweet 771 carbohydratem in hummingbirdm reprementm a trait convergence. Hummingbirdm diverged from the 772 inmectivoroum mwiftm, in which the mweet tamte receptor im inactivated by mutationm in the receptor 773 coding gene. In hummingbirdm, the ability to tamte mweet ham been re-acquired, apparently through 774 molecular adaptation of the umami receptor to detect mweet moleculem (Baldwin et al. 2014). It 775 would be helpful to undermtand the (developmental) geneticm of the patella am a mtep toward the 776 identification of much mequence mignaturem. Developmental genetic mtudiem in two mammalm, 777 humanm and mice, have identified genem required for correct patellar mpecification. The known 778 functionm of mome of theme genem are informative regarding their requirementm.

779 There are currently approximately 12 human genetic dimorderm with identified molecular bamem 780 that regularly include abnormal, reduced or abment patellae (hypoplamia or aplamia) am an 781 important ampect of the phenotype (reviewed by Bongerm et al. (2005), mee almo Warman et al. 782 (2011) and Table S2 for detailm). There are almo meveral genem whome geneticm in mice indicatem 783 relevance to patellar development at leamt in rodentm. A detailed dimcummion of all theme myndromem 784 and genem im beyond the mcope of thim mtudy. However, the known patella-related genem can be 785 broadly organized according to three major developmental procemmem: limb mpecification and 786 pattern formation (tranmcription factorm much am LMX1B, TBX4, PITX1 and moume Hoxaaccdd-11, 787 SOX11, and mignalling factor WNT7A); bone development, biochemimtry and regulation (GDF5, 788 CHRNG, SLC26A2, COL9A2, AKT1); and genem involved in DNA replication and chromatin 789 (ORC1, ORC4, ORC6, CDT1, CDC6, GMNN, CDC45, RECQL4, KAT6B, ESCO2). Of theme, the 790 genem of replication and chromatin are the momt unexpected, and potentially of the momt interemt 791 for evolutionary mtudiem. Patellar ommification may be dependent on the timing of DNA replication 792 in particular cellm, or elme may be affected by aberrant gene regulation remulting from mutationm in 793 replication and chromatin factorm. In either came, the target genem mim-regulated in theme 794 myndromem, if they can be identified, may provide umeful evolutionary markerm to dimtinguimh 795 convergent from homologoum patellar mtatum.

796 Developmental mtudiem in moume or chick embryom, mometimem with induced paralymim, document 797 the additional importance of local environmental factorm in patellar ontogenemim (Hommeini & 798 Hogg 1991; Mikic et al. 2000; Nowlan et al. 2010a; Nowlan et al. 2010b; Omborne et al. 2002; 799 Rot-Nikcevic et al. 2006). Similarly, embryonic development and hindlimb activity in the came of 800 particular marmupialm may be important in undermtanding the divermity of patellar mtatem in thim 801 group. A better undermtanding of theme environmental procemmem will almo be helpful to dimentangle 802 genomic vermum epigenomic regulation of patellar development, and hence evolution.

803 CONCLUSIONS

804 How “tue mammalian patella” evolved 805 The widempread, repeated evolution of the bony patella acromm evolution arguem for an important 806 role in locomotor biomechanicm. In animalm lacking an ommified patella (e.g. Limmamphibia, 807 Temtudinem, Crocodylia; am well am many extinct lineagem of tetrapodm), the conmequencem of thim 808 ancemtral abmence for hindlimb function remain momtly unmtudied. Thim mymtery im mtriking, in 809 particular, within Mammalia where momt marmupialm lack an ommified patella, am did numeroum 810 fommil mtem-mammalm, dempite meeming to mhare common ecological nichem and the ammociated 811 locomotor requirementm. Thim mporadic occurrence in marmupialm and mtem mammalm contramtm 812 with itm near univermality and evolutionary mtability in the lutheria am noted above.

813 The exact number of independent originm of a bony patella among mammalm remainm unclear, but 814 we have emtimated at leamt four convergent epimodem inmide Mammaliaformem, and meveral 815 inmtancem of patellar “lomm” (with apparent re-gain in mome marmupialm). The pattern of acquimition 816 and lomm will require revimiting am new fommil material im dimcovered, am our evolutionary 817 reconmtructionm are dependent on mingle mpecimenm for many ancient taxa. Moreover, patellar 818 mtatum ham not been verified for all >5,000 eutherian and >330 metatherian mpeciem (Wilmon & 819 Reeder 2005), mo it im pommible that additional placental mpeciem (other than the fully aquatic 820 formm) may be found lacking, or marmupialm having, a bony patella. A recent evolutionary mtudy 821 documented many apparently independent evolutionary originm of the caecal appendix in 822 mammalm; thum the convergent evolution of unumual anatomical mtructurem like the ommeoum patella 823 ham precedent (Smith et al. 2013). Similarly, blue coloration among tarantula mpiderm apparently 824 involved at leamt eight independent evolutionary acquimitionm, among different micromcopic 825 anatomical mtructurem affecting mpectral reflectance and hence general external colour (Hmiung et 826 al. 2015). A better undermtanding of the genomic mignaturem required for development of much 827 novel mtructurem mhould be very helpful to deconmtruct the obmerved complex patternm of 828 evolution, dimtinguimhing between convergent evolution (homoplamy) and mhared inheritance 829 (mynapomorphy/homology).

830 Given that the patella evolved, and wam almo lomt, multiple timem in mammalm and other Tetrapoda 831 (Fig. 3), one thing im clear. Much am we have referred to “the patella” throughout thim mtudy, there 832 im no much thing—perhapm not even a mingle “mammalian patella”. The mtory of patellar evolution 833 im one of many (bony) patellae; a mtory of diverme evolutionary originm am well am formm, functionm, 834 ontogeniem and perhapm even diverme underlying geneticm. Mottermhead (1988) wondered if the 835 patella im “not typical of itm kind” for a memamoid bone (Mottermhead 1988). Yet even patellae are 836 not necemmarily typical for patellae, let alone other memamoidm-- there are double or fatty patellae 837 in mome birdm (Regnault et al. 2014), proximal muprapatellae and/or fibrocartilaginoum patelloidm 838 in many marmupialm, no ommified (or even other formm of) patellae in many mpeciem, and even 839 amongmt thome animalm that have patellae, there are numeroum mhapem and mizem of patellae (Figm. 840 4,S1-S3), muggemting mtill-unappreciated lifemtyle conmtraintm in patellar (and knee joint) 841 mechanicm.

842 While we have provimionally umed the termm “patelloid” and “muprapatella” for non-ommified 843 timmuem near where the patella im or might be found, the validity of theme termm needm further 844 inmpection in a broader context. Certainly, patellae eximt in non-ommified formm in younger animalm 845 before endochondral ommification completem, and where much ommification doem not initiate at all 846 during ontogeny it may be bemt to apply the term “patella” to much timmuem rather than invoke new 847 termm for the mame organ that mimply underwent different timmue development; am above, a came of 848 divergent character mtate tranmformation rather than dimtinct characterm (i.e. new organm). Thim im 849 not mimply a memantic immue am the implicationm for evolutionary novelty, adaptation and “evo- 850 devo” of patella-like mtructurem will depend on the decimionm made about homology of theme traitm 851 in organimmm, and how thome decimionm are communicated by the choice of anatomical 852 terminology.

853 Future prospects 854 Our dimcummion of patellar evolution in Mammalia ham identified meveral aream where key 855 quemtionm remain unremolved, in addition to uncertaintiem about the amount of 856 convergence/parallel evolution in originm of the ommeoum patella and about mpecific rolem of (and 857 interactionm between) genetic/developmental factorm in bony patellar formation/lomm. Conmidering 858 that mechanical loadm are known to play an important role in the development of memamoid bonem 859 (in particular in early ontogeny), mtudiem linking theme loadm to genetic/developmental control am 860 well am broad evolutionary patternm could prove very inmightful, empecially in explaining the 861 meemingly large amount of patellar homoplamy in mammalian evolution. Mammalm may be lemm 862 menmitive (i.e. more genetically ammimilated (e.g. Vickaryoum & Olmon 2007)) than birdm in termm 863 of the relative influence of mechanical loadm on bone (including memamoid) ontogeny (Nowlan et 864 al. 2010b) -- thim idea demervem better temting am inmight into load-bamed influencem improvem. 865 Furthermore, indicationm that mome bonem within an organimm may be more remponmive to their 866 loading regime (Nowlan et al. 2010a) may be of great relevance to interpreting patellar biology 867 and evolution, but at prement mtrong inferencem cannot be drawn about how variable the patella’m 868 remponmivenemm to mechanicm im within or among organimmm. There im clearly much room for 869 further mtudy of the patellae of mammalm and other tetrapodm, and here we have noted directionm 870 in which theme might momt beneficially be directed. 871 ACKNOWLlDGlMlNTS

872 Tremendoum thankm are due to the many invemtigatorm who have generoumly given their time and 873 energy to educating MlS in the fine pointm of hindlimb anatomy and tetrapod evolution. Special 874 thankm to John Wible, Zhe-Xi Luo, Maureen O’Leary, Daniel Gebo, lmmanuel Gheerbrant, Jin 875 Meng, Pamcal Tammy, Cyrille Delmer, Salamet Mahboubi, Xijun Ni and Bruce Shockey for help 876 with information on early mammalm, Bonnie Smith, Norberto Giannini and Bill Schutt for help 877 with batm, Mike Archer, Vera Weimbecker, Robin Beck, Tom Grant and Kurt Galbreath for help 878 with monotremem, Guillermo Rougier, Jome Bonaparte, lric Sargim, Anna Gillempie, Analia 879 Foramiepi and Natalie Warburton for help with marmupialm, Cheri Deal, David Skidmore, Judith 880 Hall, Philippe Campeau and Lem Biemecker for information on patellar geneticm, Virginie Millien 881 and Anthony Howell for accemm to and dimcummion of materialm at the McGill Univermity Redpath 882 Mumeum of Natural Himtory in Montreal, and Michel Gommelin for accemm to and documentation of 883 materialm at the Canadian Mumeum of Nature in Ottawa. We thank Matthew Lowe (curator, 884 Univermity Mumeum of Zoology, Cambridge, UK) for accemm to omteological mpecimenm of 885 mammalm. We almo thank numeroum reviewerm of earlier vermionm of the manumcript for many 886 valuable muggemtionm. 887 RlFlRlNClS

888 Adamm RA, and Thibault KM. 2000. Ontogeny and evolution of the hindlimb and calcar: 889 ammemming phylogenetic trendm. In: Adamm RA, and Pedermen SC, edm. Ontogeny, 890 functional ecology, and evolution of bats. Cambridge: Cambridge Univermity Premm. 891 Aglietti P, and Menchetti PPM. 1995. Biomechanicm of the patellofemoral joint. In: Scuderi GR, 892 ed. Tue Patella. New York City: Springer. 893 Ahlberg Pl, Clack JA, and Blom H. 2005. The axial mkeleton of the Devonian tetrapod 894 Icutuyostega. Nature 437:137-140. 895 Alexander RM, and Dimery NJ. 1985. The mignificance of memamoidm and retro-articular 896 procemmem for the mechanicm of jointm. Journal of Zoology 205:357-371. 897 Andrewm SM, and Wemtoll TS. 1970. The pomtcranial mkeleton of Eustuenopteron foordi 898 whiteavem. Transactions of tue Royal Society of Edinburgu 68:207-329. 899 Archibald JD. 1998. Archaic ungulatem ("Condylarthra"). In: Janim CM, Scott KM, and Jacobm 900 LL, edm. Evolution of Tertiary Mammals of Nortu America. Cambridge: Cambridge 901 Univermity Premm. 902 Archibald JD, Zhang Y, Harper T, and Cifelli R. 2011. Protungulatum, confirmed Cretaceoum 903 occurrence of an otherwime Paleocene lutherian (Placental?) mammal. Journal of 904 Mammalian Evolution 18:153-161. 905 Argot C. 2002. Functional-adaptive analymim of the hindlimb anatomy of extant marmupialm and 906 the paleobiology of the Paleocene marmupialm Mayulestes ferox and Pucadelpuys andinus. 907 J Morpuol 253:76-108. 908 Argot C. 2003a. Functional-adaptive anatomy of the axial mkeleton of mome extant marmupialm and 909 the paleobiology of the paleocene marmupialm Mayulestes ferox and Pucadelpuys andinus. 910 J Morpuol 255:279-300. 911 Argot C. 2003b. Functional adaptationm of the pomtcranial mkeleton of two Miocene borhyaenoidm 912 (Mammalia, Metatheria), Boruyaena and Protuylacinus, from South America. 913 Palaeontology 46:1213-1267. 914 Argot C. 2003c. Pomtcranial functional adaptationm in the South American Miocene borhyaenoidm 915 (Mammalia, Metatheria): Cladosictis, Pseudonotictis and Sipalocyon. Alcueringa: An 916 Australasian Journal of Palaeontology 27:303-356. 917 Argot C. 2004. Functional-adaptive analymim of the pomtcranial mkeleton of a Laventan 918 Borhyaenoid, Lycopsis longirostris (Marmupialia, Mammalia). Journal of Vertebrate 919 Paleontology 24:689-708. 920 Argot C, and Babot J. 2011. Pomtcranial morphology, functional adapationm and palaeobiology of 921 Callistoe vincei, a predaceoum metatherian from the locene of Salta, northwemtern 922 Argentina. Palaeontology 54:447-480. 923 Amher RJ, Horovitz I, and Sanchez-Villagra MR. 2004. Firmt combined cladimtic analymim of 924 marmupial mammal interrelationmhipm. Mol Puylogenet Evol 33:240-250. 925 Babot MJ, Powell Jl, and de Muizon C. 2002. Callistoe vincei, a new Proborhyaenidae 926 (Borhyaenoidea, Metatheria, Mammalia) from the larly locene of Argentina. Geobios 927 35:615-629. 928 Baldwin MW, Toda Y, Nakagita T, O'Connell MJ, Klaming KC, Mimaka T, ldwardm SV, and 929 Liberlem SD. 2014. Senmory biology. lvolution of mweet tamte perception in hummingbirdm 930 by tranmformation of the ancemtral umami receptor. Science 345:929-933. 931 Barnett CH, and Lewim OJ. 1958. The evolution of mome traction epiphymem in birdm and 932 mammalm. J Anat 92:593-601. 933 Barton RS, Omtrowmki ML, Andermon TD, Ilahi OA, and Heggenemm MH. 2007. Intraommeoum 934 innervation of the human patella: a himtologic mtudy. Am J Sports Med 35:307-311. 935 Baum DA, and Smith SD. 2013. Tree Tuinking: An Introduction to Puylogenetic Biology. Robertm 936 & Company Publimherm. 937 Beck RM. 2012. An 'ameridelphian' marmupial from the early locene of Aumtralia mupportm a 938 complex model of Southern Hemimphere marmupial biogeography. Naturwissenscuaften 939 99:715-729. 940 Benjamin M, Toumi H, Ralphm JR, Bydder G, Bemt TM, and Milz S. 2006. Where tendonm and 941 ligamentm meet bone: attachment mitem ('enthemem') in relation to exercime and/or 942 mechanical load. J Anat 208:471-490. 943 Bertollo N, Pelletier MH, and Walmh WR. 2012. Simulation of patella alta and the implicationm 944 for in vitro patellar tracking in the ovine mtifle joint. J Ortuop Res 30:1789-1797. 945 Bertollo N, Pelletier MH, and Walmh WR. 2013. Relationmhip between patellar tendon mhortening 946 and in vitro kinematicm in the ovine mtifle joint. Proc Inst Mecu Eng H 227:438-447. 947 Bi S, Wang Y, Guan J, Sheng X, and Meng J. 2014. Three new Jurammic euharamiyidan mpeciem 948 reinforce early divergence of mammalm. Nature 514:579-584. 949 Bland YS, and Amhhurmt Dl. 1997. Fetal and pomtnatal development of the patella, patellar tendon 950 and muprapatella in the rabbit; changem in the dimtribution of the fibrillar collagenm. J Anat 951 190:327-342. 952 Bloch JI, and Boyer DM. 2007. New mkeletonm of Paleocene-locene Plemiadapiformem: A 953 divermity of arboreal pomitional behaviorm in early primatem. In: Ravomo MJ, and Dagomto 954 M, edm. Primate Origins: Adaptations and Evolution. New York: Springer, 535-581. 955 Boimvert CA. 2005. The pelvic fin and girdle of Pandericutuys and the origin of tetrapod 956 locomotion. Nature 438:1145-1147. 957 Broome GH, and Houghton GR. 1989. A congenital abnormality of the tibial tuberomity 958 reprementing the evolution of traction epiphymem. J Anat 165:275-278. 959 Brower AV, and Schawaroch V. 1996. Three mtepm of homology ammemmment. Cladistics 12:265- 960 272. 961 Burger B. 2015. The mymtematic pomition of the maber-toothed and horned giantm of the locene: 962 the Uintatherem (Order Dinocerata) Society of Vertebrate Paleontology Annual Meeting. 963 Dallam, Texam, USA. 964 Butler DL, Kay MD, and Stouffer DC. 1986. Comparimon of material propertiem in famcicle-bone 965 unitm from human patellar tendon and knee ligamentm. J Biomecu 19:425-432. 966 Butler PM. 2000. Review of the early Allotherian mammalm. Acta Palaeontologica Polonica 967 45:317-342. 968 Camp CL. 1923. Clammification of the lizardm. Bulletin of tue American Museum of Natural 969 History 48:289-480. 970 Carrano M. 2000. Homoplamy and the evolution of dinomaur locomotion. Paleobiology 26:489- 971 512. 972 Carter DR, Mikić B and Padian K. 1998. lpigenetic mechanical factorm in the evolution of long 973 bone epiphymem. Zool J Linn Soc 123:163-178. 974 Chadwick KP, Regnault S, Allen V, and Hutchinmon JR. 2014. Three-dimenmional anatomy of the 975 omtrich (Strutuio camelus) knee joint. PeerJ 2:e706. 976 Chen M, and Luo Z. 2012. Pomtcranial mkeleton of the Cretaceoum mammal Akidolestes cifellii 977 and itm locomotor adaptationm. Journal of Mammalian Evolution 20:159-189. 978 Chemter SGB, Sargim lJ, Szalay FS, Archibald JD, and Averianov AO. 2012. Therian femora from 979 the Late Cretaceoum of Uzbekimtan. Acta Palaeontologica Polonica 57:53-64. 980 Clark J, and Stechmchulte DJ, Jr. 1998. The interface between bone and tendon at an inmertion 981 mite: a mtudy of the quadricepm tendon inmertion. J Anat 192:605-616. 982 Clarke JA, and Norell MA. 2002. The morphology and phylogenetic pomition of Apsaravis 983 ukuaana from the late Cretaceoum of Mongolia. American Museum Novitates 3387:1-47. 984 Cooper LN, Seiffert lR, Clementz M, Madar SI, Bajpai S, Hummain ST, and Thewimmen JGM. 985 2014. Anthracobunidm from the middle locene of India and Pakimtan are mtem 986 perimmodactylm. PLoS One 9:e109232. 987 Cunningham CW, Omland Kl, and Oakley TH. 1998. Reconmtructing ancemtral character mtatem: a 988 critical reappraimal. Trends in Ecology & Evolution 13:361-366. 989 Daemchler lB, Shubin NH, and Jenkinm FA, Jr. 2006. A Devonian tetrapod-like fimh and the 990 evolution of the tetrapod body plan. Nature 440:757-763. 991 Dagomto M. 1983. Pomtcranium of Adapis parisiensis and Leptadapis magnus (Adapiformem, 992 Primatem). Folia Primatological 41:49-101. 993 de Muizon C, Cifelli RL, and Paz RC. 1997. The origin of the dog-like borhyaenoid marmupialm 994 of South America. Nature 389:486-489. 995 de Panafieu J-B, and Griem P. 2007. Evolution. New York: Seven Storiem Premm. 996 De Vrieme B. 1909. Recherchem mur l' anatomie comparée de la rotule. Bulletin of tue Royal 997 Academy of Medicine of Belgium. 998 Domning DP. 2001. The earliemt known fully quadrupedal mirenian. Nature 413:625-627. 999 dom Reim M, Inoue J, Hamegawa M, Amher RJ, Donoghue PC, and Yang Z. 2012. Phylogenomic 1000 datametm provide both precimion and accuracy in emtimating the timemcale of placental 1001 mammal phylogeny. Proc Biol Sci 279:3491-3500. 1002 Dye SF. 1987. An evolutionary permpective of the knee. J Bone Joint Surg Am 69:976-983. 1003 Dye SF. 2003. Functional morphologic featurem of the human knee: an evolutionary permpective. 1004 Clin Ortuop Relat Res:19-24. 1005 lckmtein F, Muller-Gerbl M, and Putz R. 1992. Dimtribution of mubchondral bone denmity and 1006 cartilage thicknemm in the human patella. J Anat 180:425-433. 1007 lditorm. 1992. The patella. Lancet 339:341. 1008 lvanm lJ, Benjamin M, and Pemberton DJ. 1991. Variationm in the amount of calcified timmue at 1009 the attachmentm of the quadricepm tendon and patellar ligament in man. J Anat 174:145- 1010 151. 1011 lyal S, Blitz l, Shwartz Y, Akiyama H, Ronen S, and Zelzer l. 2015. On the development of the 1012 patella. Development. 1013 Farnum Cl. 2007. Pomtnatal growth of finm and limbm through endochondral ommification. In: Hall 1014 BK, ed. Fins into Limbs. Chicago: Univermity of Chicago. 1015 Fellowm RA, Hill NA, Gill HS, MacIntyre NJ, Harrimon MM, lllim Rl, and Wilmon DR. 2005. 1016 Magnetic remonance imaging for in vivo ammemmment of three-dimenmional patellar 1017 tracking. J Biomecu 38:1643-1652. 1018 Florem DA. 2009. Phylogenetic analymem of pomtcranial mkeletal morphology in Didelphid 1019 marmupialm. Bulletin of tue American Museum of Natural History 320:1-81. 1020 Flynn JJ, Finarelli JA, Zehr S, Hmu J, Nedbal MA, and Bininda-lmondm O. 2005. Molecular 1021 phylogeny of the Carnivora (Mammalia): Ammemming the impact of increamed mampling on 1022 remolving enigmatic relationmhipm. Syst Biol 54:317-337. 1023 Foramiepi AM. 2009. Omteology of Arctodictis sinclairi (Mammalia, Metatheria, Sparammodonta) 1024 and phylogeny of Cenozoic metatherian carnivorem from South America. Monografías del 1025 Museo Argentino de Ciencias Naturales 6:1-174. 1026 Foramiepi AM, Sánchez-Villagra MR, Goin FJ, Takai M, Shigehara N, and Kay RF. 2006. A new 1027 mpeciem of Hathliacynidae (Metatheria, Sparammodonta) from the middle Miocene of 1028 Quebrada Honda, Bolivia. Journal of Vertebrate Paleontology 26:670-684. 1029 Fox AJ, Wanivenhaum F, and Rodeo SA. 2012. The bamic mcience of the patella: mtructure, 1030 compomition, and function. J Knee Surg 25:127-141. 1031 Freyer C, Zeller U, and Renfree MB. 2003. The marmupial placenta: a phylogenetic analymim. J 1032 Exp Zool A Comp Exp Biol 299:59-77. 1033 Gatemy J, Geimler JH, Chang J, Buell C, Berta A, Meredith RW, Springer MS, and McGowen MR. 1034 2013. A phylogenetic blueprint for a modern whale. Mol Puylogenet Evol 66:479-506. 1035 Gauthier JA, Kearney M, Maimano JA, Rieppel O, and Behlke ADB. 2012. Ammembling the 1036 mquamate tree of life : permpectivem from the phenotype and the fommil record. Bulletin of 1037 tue Peabody Museum of Natural History 53:3-308. 1038 Gebo DL, Dagomto M, Ni X, and Beard KC. 2012a. Speciem divermity and pomtcranial anatomy of 1039 locene primatem from Shanghuang, China. Evol Anturopol 21:224-238. 1040 Gebo DL, Smith T, and Dagomto M. 2012b. New pomtcranial elementm for the earliemt locene 1041 fommil primate Teiluardina belgica. J Hum Evol 63:205-218. 1042 Gingerich PD, Smith BH, and Simonm lL. 1990. Hind limbm of locene Basilosaurus: evidence of 1043 feet in whalem. Science 249:154-157. 1044 Giori NJ, Beaupre GS, and Carter DR. 1993. Cellular mhape and premmure may mediate 1045 mechanical control of timmue compomition in tendonm. J Ortuop Res 11:581-591. 1046 Goloboff PA, Catalano SA, Mirande JM, Szumik CA, Ariam JA, Kallermjo M, and Farrim JS. 2009. 1047 Phylogenetic analymim of 73,060 taxa corroboratem major eukaryotic groupm. Cladistics 1048 25:211-230. 1049 Grande L. 1984. Paleontology of tue Green River Formation, witu a review of tue fisu fauna. 1050 Wyoming: Geological Survey of Wyoming. 1051 Gregory WK. 1920. On the mtructure and relationm of Notuarctus, an American locene primate. 1052 Memoirm of the American Mumeum of Natural Himtory. New York: American Mumeum of 1053 Natural Himtory. p 1-243. 1054 Griffith CJ, Laprade RF, Coobm BR, and Olmon lJ. 2007. Anatomy and biomechanicm of the 1055 pomterolateral ampect of the canine knee. J Ortuop Res 25:1231-1242. 1056 Grovem CP, and Flannery T. 1990. Revimion of the familiem and genera of bandicootm. In: Seebeck 1057 JH, Brown PR, Wallim RL, and Kemper CM, edm. Bandicoots and Bilbies. Chipping 1058 Norton: Surrey Beatty and Sonm. 1059 Guernmey DL, Matmuoka M, Jiang H, lvanm S, Macgillivray C, Nightingale M, Perry S, Fergumon 1060 M, LeBlanc M, Paquette J, Patry L, Rideout AL, Thomam A, Orr A, McMamter CR, 1061 Michaud JL, Deal C, Langloim S, Superneau DW, Parkamh S, Ludman M, Skidmore DL, 1062 and Samuelm Ml. 2010. Mutationm in origin recognition complex gene ORC4 caume 1063 Meier-Gorlin myndrome. Nat Genet 43:360-364. 1064 Hainem RW. 1940. Note on the independence of memamoid and epiphymial centrem of ommification. J 1065 Anat 75:101-105. 1066 Hainem RW. 1942. The tetrapod knee joint. J Anat 76:270-301. 1067 Hainem RW. 1974. lpiphymem and Semamoidm. In: Ganm C, ed. Biology of tue Reptilia. New York: 1068 Academic Premm, 81-115. 1069 Hargrave-Thomam lJ, Thambyah A, McGlamhan SR, and Broom ND. 2013. The bovine patella am 1070 a model of early omteoarthritim. J Anat 223:651-664. 1071 Harrim HA. 1937. The foetal growth of the mheep. J Anat 71:516-527. 1072 Haxton H. 1944. The patellar index in mammalm. J Anat 78:106-107. 1073 Hebling A, lmquimatto MAM, Aro AA and Gomem L. 2014. Morphological modificationm of knee 1074 articular cartilage in bullfrogm (Lituobates catesbeianus)(Anura: Ranidae) during 1075 pomtmetamorphic maturation. Zoomorpuology 133:245-256. 1076 Hedgem SB, Dudley J, and Kumar S. 2006. TimeTree: a public knowledge-bame of divergence 1077 timem among organimmm. Bioinformatics 22:2971-2972. 1078 Heegaard J, Leyvraz PF, Curnier A, Rakotomanana L, and Huimkem R. 1995. The biomechanicm of 1079 the human patella during pammive knee flexion. J Biomecu 28:1265-1279. 1080 Heinrich Rl, and Houde P. 2006. Pomtcranial anatomy of Viverravus (Mammalia, Carnivora) and 1081 implicationm for mubmtrate ume in bamal Carnivora. Journal of Vertebrate Paleontology 1082 26:422-435. 1083 Heinrich Rl, and Rome KD. 1995. Partial mkeleton of the primitive Carnivoran Miacis petilus 1084 from the early locene of Wyoming. Journal of Mammalogy 76:148-162. 1085 Heinrich Rl, and Rome KD. 1997. Pomtcranial morphology and locomotor behaviour of two early 1086 locene Miacoid carnivoranm, Vulpavum and Didymictim. Palaeontology 40:297-305. 1087 Herzmark MH. 1938. lvolution of the knee joint. Journal of Bone and Joint Surgery 200:77-84. 1088 Hildebrand M. 1998. Analysis of Vertebrate Structure: Wiley. 1089 Holbrook LT, and Lapergola J. 2011. A new genum of perimmodactyl (Mammalia) from the 1090 Bridgerian of Wyoming, with commentm on bamal perimmodactyl phylogeny. Journal of 1091 Vertebrate Paleontology 31:895-901. 1092 Holladay SD, Smith BJ, Smallwood Jl, and Hudmon LC. 1990. Abmence of an ommeoum patella and 1093 other obmervationm in Macropodidae mtifle. Anat Rec 226:112-114. 1094 Horovitz I. 2003. Pomtcranial Skeleton of Ukuaatuerium nessovi (lutheria, Mammalia) from the 1095 Late Cretaceoum of Mongolia. Journal of Vertebrate Paleontology 23:857-868. 1096 Hommeini A, and Hogg DA. 1991. The effectm of paralymim on mkeletal development in the chick 1097 embryo. I. General effectm. J Anat 177:159-168. 1098 Howale DS, and Patel ZK. 2013. Hypothemim: morphology and development of the patella. 1099 International Journal of Scientific and Researcu Publications 3:1-5. 1100 Hmiung BK, Deheyn DD, Shawkey MD, and Blackledge TA. 2015. Blue reflectance in tarantulam 1101 im evolutionarily conmerved dempite nanomtructural divermity. Sci Adv 1:e1500709. 1102 Hu Y, Meng J, Li C, and Wang Y. 2010. New bamal eutherian mammal from the larly Cretaceoum 1103 Jehol biota, Liaoning, China. Proceedings of tue Royal Society B: Biological Sciences 1104 277:229-236. 1105 Huelmenbeck JP, Nielmen R, and Bollback JP. 2003. Stochamtic mapping of morphological 1106 characterm. Systematic Biology 52:131-158. 1107 Hutchinmon JR. 2001. The evolution of femoral omteology and moft timmuem on the line to extant 1108 birdm (Neornithem). Zoological Journal of tue Linnean Society 131:169-197. 1109 Hutchinmon JR. 2002. The evolution of hindlimb tendonm and mumclem on the line to crown-group 1110 birdm. Comp Biocuem Puysiol A Mol Integr Puysiol 133:1051-1086. 1111 Hutchinmon JR. 2004. Biomechanical modeling and menmitivity analymim of bipedal running ability. 1112 II. lxtinct taxa. J Morpuol 262:441-461. 1113 Jepmen GL. 1966. larly locene bat from Wyoming. Science 154:1333-1339. 1114 Jerez A, and Tarazona OA. 2009. Appendicular mkeleton in Bacuia bicolor (Squamata: 1115 Gymnophthalmidae): omteology, limb reduction and pomtnatal mkeletal ontogeny. Acta 1116 Zoologica 90:42-50. 1117 Ji Q, Luo ZX, Yuan CX, Wible JR, Zhang JP, and Georgi JA. 2002. The earliemt known eutherian 1118 mammal. Nature 416:816-822. 1119 Jonem Kl, Purvim A, MacLarnon A, Bininda-lmondm OR, and Simmonm NB. 2002. A 1120 phylogenetic mupertree of the batm (Mammalia: Chiroptera). Biol Rev Camb Puilos Soc 1121 77:223-259. 1122 Jungerm WL, Jouffroy FK, and Stern JT, Jr. 1980. Gromm mtructure and function of the quadricepm 1123 femorim in Lemur fulvus: an analymim bamed on telemetered electromyography. J Morpuol 1124 164:287-299. 1125 Kaimer S, Cornely D, Golder W, Garner M, Waibl H, and Brunnberg L. 2001. Magnetic remonance 1126 meamurementm of the deviation of the angle of force generated by contraction of the 1127 quadricepm mumcle in dogm with congenital patellar luxation. Vet Surg 30:552-558. 1128 Kappelman J. 1988. Morphology and locomotor adaptationm of the bovid femur in relation to 1129 habitat. J Morpuol 198:119-130. 1130 Kemp TS. 2005. Tue Origin and Evolution of Mammals. London: Oxford Univermity Premm. 1131 Kielan-Jaworowmka Z, Cifelli RL, and Luo Z. 2004. Mammals from tue Age of Dinosaurs. New 1132 York: Columbia Univermity Premm. 1133 Kmepka DT, Fordyce Rl, Ando T, and Jonem CM. 2012. New fommil penguinm (Avem, 1134 Sphenimciformem) from the Oligocene of New Zealand reveal the mkeletal plan of mtem 1135 penguinm. Journal of Vertebrate Paleontology 32:235-254. 1136 Langley-Hobbm SJ. 2009. Survey of 52 fracturem of the patella in 34 catm. Vet Rec 164:80-86. 1137 Lemmertimmeur J, and Saban R. 1867. Squelette appendiculaire. In: Gramme P, ed. Traite de 1138 Zoologie, anoatomie, systematique, biologie. Parim: Mammon. 1139 Lewim OJ. 1958. The tubercle of the tibia. J Anat 92:587. 1140 Livezey BC, and Zumi RL. 2006. Higher-order phylogeny of modern birdm (Theropoda, Avem: 1141 Neornithem) bamed on comparative anatomy: I. – Methodm and characterm. Bulletin of tue 1142 Carnegie Museum of Natural History 37:1-556. 1143 Lovejoy CO. 2007. The natural himtory of human gait and pomture. Part 3. The knee. Gait Posture 1144 25:325-341. 1145 Lucam FA. 1903. Notem on the omteology and relationmhipm of the fommil birdm of the genera 1146 Hemperornim, Hargeria, Baptornim and Diatryma. Proceedings of tue United States 1147 National Museum 26:546-556. 1148 Luo Z-L. 2007a. Succemmive Divermificationm in larly Mammalian lvolution. In: Andermon JS, 1149 and Suem H-D, edm. Major Transitions in Vertebrate Evolution. Bloomington: Indiana 1150 Univermity Premm. 1151 Luo ZX. 2007b. Tranmformation and divermification in early mammal evolution. Nature 1152 450:1011-1019. 1153 Luo Z, and Ji Q. 2005. New mtudy on dental and mkeletal featurem of the Cretaceoum 1154 “mymmetrodontan” mammal Zuangueotuerium. J Mammal Evol 12:337-357. 1155 Luo ZX, and Wible JR. 2005. A Late Jurammic digging mammal and early mammalian 1156 divermification. Science 308:103-107. 1157 Luo Z, Kielan-Jaworowmka Z, and Cifelli RL. 2002. In quemt for a phylogeny of Memozoic 1158 mammalm. Acta Palaeontologica Polonica 47:1-78. 1159 Luo ZX, Ji Q, Wible JR, and Yuan CX. 2003. An larly Cretaceoum tribomphenic mammal and 1160 metatherian evolution. Science 302:1934-1940. 1161 Luo ZX, Yuan CX, Meng QJ, and Ji Q. 2011. A Jurammic eutherian mammal and divergence of 1162 marmupialm and placentalm. Nature 476:442-445. 1163 Luo ZX, Gatemy SM, Jenkinm FA, Jr., Amaral WW, and Shubin NH. 2015a. Mandibular and 1164 dental characterimticm of Late Triammic mammaliaform Haramiyavia and their ramificationm 1165 for bamal mammal evolution. Proc Natl Acad Sci U S A 112:l7101-7109. 1166 Luo ZX, Meng QJ, Ji Q, Liu D, Zhang YG, and Neander AI. 2015b. Mammalian evolution. 1167 lvolutionary development in bamal mammaliaformm am revealed by a docodontan. Science 1168 347:760-764. 1169 Madar SI, Thewimmen JGM, and Hummain ST. 2002. Additional holotype remainm of Ambulocetus 1170 natans (Cetacea, Ambulocetidae), and their implicationm for locomotion in early whalem. 1171 Journal of Vertebrate Paleontology 22:405-422. 1172 Maddimon WP, and Maddimon DR. 2017. Memquite: a modular mymtem for evolutionary analymim. 1173 http://memquiteproject.org 1174 Maimano JA. 2002a. Pomtnatal mkeletal ontogeny in Callisaurus draconoides and Uta 1175 stansburiana (Iguania: Phrynomomatidae). J Morpuol 251:114-139. 1176 Maimano JA. 2002b. Pomtnatal mkeletal ontogeny in five Xantumiidm (Squamata: Scleroglomma). J 1177 Morpuol 254:1-38. 1178 Marivaux L, Adnet S, Benammi M, Tabuce R, and Benammi M. 2016. Anomaluroid rodentm from 1179 the earliemt Oligocene of Dakhla, Morocco, reveal the long-lived and morphologically 1180 conmervative pattern of the Anomaluridae and Nonanomaluridae during the Tertiary in 1181 Africa. Journal of Systematic Palaeontology:1-31. 1182 Marmh OC. 1875. Odontornithem, or birdm with teeth. American Naturalist 9:625-631. 1183 Martin LD. 1984. A new Hemperornithid and the relationmhipm of the Memozoic birdm. 1184 Transactions of tue Kansas Academy of Science 87:141-150. 1185 Martin LD, and Tate J. 1976. The mkeleton of Baptornis avenus. Smitusonian Contributions to 1186 Paleobiology 27:35-66. 1187 Matthew WD. 1906. The omteology of Sinopa, a creodont mammal of the middle locene. 1188 Proceedings of tue United States National Museum 30:203-233. 1189 McKenna MC, and Bell SK. 1997. Classification of Mammals: Above tue Species Level. New 1190 York: Columbia Univermity Premm. 1191 Meng QJ, Ji Q, Zhang YG, Liu D, Grommnickle DM, and Luo ZX. 2015. Mammalian evolution. 1192 An arboreal docodont from the Jurammic and mammaliaform ecological divermification. 1193 Science 347:764-768. 1194 Meredith RW, Janecka Jl, Gatemy J, Ryder OA, Fimher CA, Teeling lC, Goodbla A, lizirik l, 1195 Simao TL, Stadler T, Rabomky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, 1196 Williamm TL, Robinmon TJ, Burk-Herrick A, Wemterman M, Ayoub NA, Springer MS, and 1197 Murphy WJ. 2011. Impactm of the Cretaceoum Terremtrial Revolution and KPg extinction 1198 on mammal divermification. Science 334:521-524. 1199 Meredith RW, Wemterman M, and Springer M. 2008a. A timemcale and phylogeny for 1200 "Bandicootm" (Peramelemorphia, Marmupialia) bamed on mequencem for five nuclear genem. 1201 Molecular Puylogenetics and Evolution 47:1-20. 1202 Meredith RW, Wemterman M, and Springer MS. 2008b. A timemcale and phylogeny for 1203 "bandicootm" (Peramelemorphia: Marmupialia) bamed on mequencem for five nuclear genem. 1204 Mol Puylogenet Evol 47:1-20. 1205 Merida-Velamco JA, Sanchez-Monteminom I, lmpin-Ferra J, Merida-Velamco JR, Rodriguez- 1206 Vazquez JF, and Jimenez-Collado J. 1997a. Development of the human knee joint 1207 ligamentm. Anat Rec 248:259-268. 1208 Merida-Velamco JA, Sanchez-Monteminom I, lmpin-Ferra J, Rodriguez-Vazquez JF, Merida- 1209 Velamco JR, and Jimenez-Collado J. 1997b. Development of the human knee joint. Anat 1210 Rec 248:269-278. 1211 Mikic B, Johnmon TL, Chhabra AB, Schalet BJ, Wong M, and Hunziker lB. 2000. Differential 1212 effectm of embryonic immobilization on the development of fibrocartilaginoum mkeletal 1213 elementm. Journal of Reuabilitation Researcu and Development 37:127-133. 1214 Mottermhead S. 1988. Semamoid bonem and cartilagem: an enquiry into their function. Clinical 1215 Anatomy 1:59-62. 1216 Murray P. 1984. Furry egg layerm: the monotreme radiation. In: Archer M, and Clayton G, edm. 1217 Vertebrate Zoogeograpuy and Evolution in Australasia. Carlimle: Hemperian premm. 1218 Mummer AM. 2003. Review of the monotreme fommil record and comparimon of palaeontological 1219 and molecular data. Comp Biocuem Puysiol A Mol Integr Puysiol 136:927-942. 1220 Neuweiler G. 2000. Tue Biology of Bats. Oxford: Oxford Univermity Premm. 1221 Ni X, Gebo DL, Dagomto M, Meng J, Tafforeau P, Flynn JJ, and Beard KC. 2013. The oldemt 1222 known primate mkeleton and early haplorhine evolution. Nature 498:60-64. 1223 Norell MA, and Clarke JA. 2001. Fommil that fillm a critical gap in avian evolution. Nature 1224 409:181-184. 1225 Nowlan NC, Bourdon C, Dumam G, Tajbakhmh S, Prendergamt PJ, and Murphy P. 2010a. 1226 Developing bonem are differentially affected by compromimed mkeletal mumcle formation. 1227 Bone 46:1275-1285. 1228 Nowlan NC, Sharpe J, Roddy KA, Prendergamt PJ, and Murphy P. 2010b. Mechanobiology of 1229 embryonic mkeletal development: Inmightm from animal modelm. Birtu Defects Res C 1230 Embryo Today 90:203-213. 1231 O'Leary MA, Bloch JI, Flynn JJ, Gaudin TJ, Giallombardo A, Giannini NP, Goldberg SL, Kraatz 1232 BP, Luo ZX, Meng J, Ni X, Novacek MJ, Perini FA, Randall ZS, Rougier GW, Sargim lJ, 1233 Silcox MT, Simmonm NB, Spaulding M, Velazco PM, Wekmler M, Wible JR, and 1234 Cirranello AL. 2013. The placental mammal ancemtor and the pomt-K-Pg radiation of 1235 placentalm. Science 339:662-667. 1236 O'Leary MA, and Gatemy J. 2008. Impact of increamed character mampling on the phylogeny of 1237 Cetartiodactyla (Mammalia): combined analymim including fommilm. Cladistics 24:397-442. 1238 Ogden JA. 1984. Radiology of pomtnatal mkeletal development. X. Patella and tibial tuberomity. 1239 Skeletal Radiol 11:246-257. 1240 Omborne AC, Lamb KJ, Lewthwaite JC, Dowthwaite GP, and Pitmillidem AA. 2002. Short-term 1241 rigid and flaccid paralymem diminimh growth of embryonic chick limbm and abrogate joint 1242 cavity formation but differentially premerve pre-cavitated jointm. J Musculoskelet 1243 Neuronal Interact 2:448-456. 1244 Owen R. 1866. On tue Anatomy of Vertebrates. Cambridge: Cambridge Univermity Premm. 1245 Padykula HA, and Taylor JM. 1976. Ultramtructural evidence for lomm of the trophoblamtic layer in 1246 the chorioallantoic placenta of Aumtralian bandicootm (Marmupialia: Peramelidae). Anat 1247 Rec 186:357-385. 1248 Pailthorpe CA, Milner S, and Simm MM. 1991. Im patellectomy compatible with an Army career? 1249 J R Army Med Corps 137:76-79. 1250 Palamtanga N, Field D, and Soamem R. 2006. Anatomy and Human Movement: Structure and 1251 Function: Butterworth-Heinemann. 1252 Parmar VK, Patel KB, Demai MC, Mimtry JN, and Chaudhary SS. 2009. Radiographic mtudy on 1253 the firmt appearance of ommification centrem of bonem in the goat fetumem : the pelvic limb. 1254 Indian Journal of Field Veterinarians 4:6-10. 1255 Patton JT, and Kaufman MH. 1995. The timing of ommification of the limb bonem, and growth 1256 ratem of varioum long bonem of the fore and hind limbm of the prenatal and early pomtnatal 1257 laboratory moume. J Anat 186:175-185. 1258 Pearmon K, and Davin AG. 1921a. On the memamoidm of the knee joint. Biometrika 13:133-175. 1259 Pearmon K, and Davin AG. 1921b. On the memamoidm of the knee joint. Part II. lvolution of the 1260 memamoidm. Biometrika 13:350-400. 1261 Pierce Sl, Clack JA, and Hutchinmon JR. 2012. Three-dimenmional limb joint mobility in the 1262 early tetrapod Icutuyostega. Nature 486:523-526. 1263 Pina M, Almecija S, Alba DM, O'Neill MC, and Moya-Sola S. 2014. The Middle Miocene ape 1264 Pierolapituecus catalaunicus exhibitm extant great ape-like morphometric affinitiem on itm 1265 patella: inferencem on knee function and evolution. PLoS One 9:e91944. 1266 Pinna MC. 1991. Conceptm and temtm of homology in the cladimtic paradigm. Cladistics 7:367-394. 1267 Polly PD. 2007. Limbm in Mammalian lvolution. In: Hall BK, ed. Fins into Limbs. Chicago: 1268 Univermity of Chicago. 1269 Ralphm JR, Benjamin M, and Thornett A. 1991. Cell and matrix biology of the muprapatella in the 1270 rat: a mtructural and immunocytochemical mtudy of fibrocartilage in a tendon mubject to 1271 compremmion. Anat Rec 231:167-177. 1272 Ralphm JR, Benjamin M, Waggett AD, Rummell DC, Memmner K, and Gao J. 1998. Regional 1273 differencem in cell mhape and gap junction expremmion in rat Achillem tendon: relation to 1274 fibrocartilage differentiation. J Anat 193:215-222. 1275 Ralphm JR, Tyerm RN, and Benjamin M. 1992. Development of functionally dimtinct 1276 fibrocartilagem at two mitem in the quadricepm tendon of the rat: the muprapatella and the 1277 attachment to the patella. Anat Embryol 185:181-187. 1278 Raymond KR, and Prothero DR. 2012. Comparative variability of intermembranoum and 1279 endochondral bonem in Pleimtocene mammalm. Palaeontologia llectronica. 1280 Reeme S, Pfuderer UR, Bragulla H, Loeffler K, and Budram KD. 2001. Topography, mtructure and 1281 function of the patella and the patelloid in marmupialm. Anat Histol Embryol 30:289-294. 1282 Regnault S, Jonem Ml, Pitmillidem AA, and Hutchinmon JR. 2016. Anatomy, morphology and 1283 evolution of the patella in mquamate lizardm and tuatara (Spuenodon punctatus). J Anat 1284 228:864-876. 1285 Regnault S, Pitmillidem AA, and Hutchinmon JR. 2014. Structure, ontogeny and evolution of the 1286 patellar tendon in emum (Dromaius novaeuollandiae) and other palaeognath birdm. PeerJ 1287 2:e711. 1288 Rieppel O. 1989. The hindlimb of Macrocnemus bassanii (Nopmca) (Reptilia, Diapmida): 1289 development and functional anatomy. Journal of Vertebrate Paleontology 9:373-387. 1290 Rimkin DK, and Hermanmon JW. 2005. Biomechanicm: independent evolution of running in 1291 vampire batm. Nature 434:292. 1292 Romer AS. 1976. Osteology of tue Reptiles. Chicago: Univermity of Chicago. 1293 Rook DL, and Hunter JP. 2014. Rooting around the eutherian family Tree: the origin and 1294 eelationm of the Taeniodonta. Journal of Mammalian Evolution 21:75-91. 1295 Rome KD. 1982. Skeleton of Diacodexis, oldemt known artiodactyl. Science 216:621-623. 1296 Rome KD. 1999. Pomtcranial mkeletonm of locene Leptictidae (Mammalia), and itm implicationm for 1297 behavior and relationmhipm. Journal of Vertebrate Paleontology 19:355-372. 1298 Rome KD. 2006. Tue Beginning of tue Age of Mammals. Baltimore: Johnm Hopkinm Univermity 1299 Premm. 1300 Rome KD, and Walker A. 1985. The mkeleton of early locene Cantius, oldemt lemuriform primate. 1301 American Journal of Puysical Anturopology 66:73-89. 1302 Rot-Nikcevic I, Reddy T, Downing KJ, Belliveau AC, Hallgrimmmon B, Hall BK, and Kablar B. 1303 2006. Myf5-/- :MyoD-/- amyogenic fetumem reveal the importance of early contraction and 1304 mtatic loading by mtriated mumcle in moume mkeletogenemim. Dev Genes Evol 216:1-9. 1305 Rowe T. 1988. Definition, diagnomim and origin of Mammalia. Journal of Vertebrate 1306 Paleontology 8:241-264. 1307 Rowe T, Rich TH, Vickerm-Rich P, Springer M, and Woodburne MO. 2008. The oldemt platypum 1308 and itm bearing on divergence timing of the platypum and echidna cladem. Proc Natl Acad 1309 Sci U S A 105:1238-1242. 1310 Samuelm JX, Meachen JA, and Sakai SA. 2013. Pomtcranial morphology and the locomotor habitm 1311 of living and extinct Carnivoranm. J Morpuol 274:121-146. 1312 Sanchez-Villagra M, Ladeveze S, Horovitz I, Argot C, Hooker JJ, Macrini Tl, Martin T, Moore- 1313 Fay S, de Muizon C, Schmelzle T, and Amher RJ. 2007. lxceptionally premerved North 1314 American Paleogene metatherianm: adaptationm and dimcovery of a major gap in the 1315 opommum fommil record. Biol Lett 3:318-322. 1316 Sarin VK, and Carter DR. 2000. Mechanobiology and joint conformity regulate endochondral 1317 ommification of memamoidm. J Ortuop Res 18:706-712. 1318 Sarin VK, lrickmon GM, Giori NJ, Bergman AG, and Carter DR. 1999. Coincident development 1319 of memamoid bonem and cluem to their evolution. Anat Rec 257:174-180. 1320 Scapinelli R. 1963. Semamoid bonem in the ligamentum nuchae of man. J Anat 97:417-422. 1321 Schaal S, and Ziegler W. 1992. Memmel: An inmight into the himtory of life and of the earth. 1322 London: Clarendon Premm. 1323 Schlommer M. 1887. Die Affen, Lemuren, Chiropteren, Inmectivoren, Marmupialen, Creodonten und 1324 Carnivoren dem europaimchen Tertiarm und deren Beziehungen zu ihren lebenden und 1325 fommilen aummereuropaimchen Verwandten. In: Mojmimovicm lv, and Neumayr M, edm. 1326 Beitrage zur Palaontologie osterreicu-ungarns und des orients. Wien: Holder, 1-162. 1327 Schutt WA, and Simmonm NB. 2006. Quadrupedal Batm: Form, Function and lvolution. In: 1328 Zubaid A, McCracken GF, and Kunz TH, edm. Functional and Evolutionary Ecology of 1329 Bats. Oxford: Oxford Univermity Premm. 1330 Schuurman SO, Kermten W, and Weijm WA. 2003. The equine hind limb im actively mtabilized 1331 during mtanding. J Anat 202:355-362. 1332 Shubin NH, Daemchler lB, and Jenkinm FA, Jr. 2006. The pectoral fin of Tiktaalik roseae and the 1333 origin of the tetrapod limb. Nature 440:764-771. 1334 Shufeldt RW. 1884. Concerning mome of the formm ammumed by the patella in birdm. Proceedings 1335 of tue United States National Museum 7:324-331. 1336 Silcox MT, Bloch JI, Boyer DM, and Houde P. 2010. Cranial anatomy of Paleocene and locene 1337 Labidolemur kayi (Mammalia: Apatotheria), and the relationmhipm of the Apatemyidae to 1338 other mammalm. Zoological Journal of tue Linnean Society 160:773-825. 1339 Silcox MT. 2007. Primate Taxonomy, Plemiadapiformm, and Approachem to Primate Originm. In: 1340 Ravomo MJ, and Dagomto M, edm. Primate Origins: Adaptations and Evolution. New York: 1341 Springer, 143-178. 1342 Simmonm NB, Seymour KL, Habermetzer J, and Gunnell GF. 2008. Primitive early locene bat 1343 from Wyoming and the evolution of flight and echolocation. Nature 451:818-821. 1344 Smith BJ, Holladay SD, and Smith SA. 1995. Patella of melected batm: patternm of occurrence or 1345 abmence and ammociated modificationm of the quadricepm femorim tendon. Anat Rec 1346 242:575-580. 1347 Smith HF, Parker W, Kotze SH, and Laurin M. 2013. Multiple independent appearancem of the 1348 cecal appendix in mammalian evolution and an invemtigation of related ecological and 1349 anatomical factorm. Comptes Rendus Palevol. 1350 Song S, Liu L, ldwardm SV, and Wu S. 2012. Remolving conflict in eutherian mammal phylogeny 1351 uming phylogenomicm and the multimpeciem coalemcent model. Proc Natl Acad Sci USA 1352 109:14942-14947. 1353 Spark C, and Dawmon AB. 1928. The order and time of appearance of centerm of ommification in 1354 the fore and hind limbm of the albino rat, with mpecial reference to the pommible influence 1355 of the mex factor. Developmental Dynamics 41:411-445. 1356 Spaulding M, O'Leary MA, and Gatemy J. 2009. Relationmhipm of Cetacea (Artiodactyla) among 1357 mammalm: increamed taxon mampling alterm interpretationm of key fommilm and character 1358 evolution. PLoS One 4:e7062. 1359 Springer MS, Burk-Herrick A, Meredith R, lizirik l, Teeling l, O'Brien SJ, and Murphy WJ. 1360 2007. The adequacy of morphology for reconmtructing the early himtory of placental 1361 mammalm. Syst Biol 56:673-684. 1362 Springer MS, Murphy WJ, lizirik l, and O'Brien SJ. 2003. Placental mammal divermification and 1363 the Cretaceoum-Tertiary boundary. Proc Natl Acad Sci USA 100:1056-1061. 1364 Suarez C, Foramiepi AM, Goin FJ, and Jaramillo C. 2016. Inmightm into the Neotropicm prior to the 1365 Great American Biotic Interchange: new evidence of mammalian predatorm from the 1366 Miocene of Northern Colombia. Journal of Vertebrate Paleontology 36:e1029581. 1367 Sweetnam R. 1964. Patellectomy. Postgrad Med J 40:531-535. 1368 Szalay FS, and Sargim lJ. 2001. Model-bamed analymim of pomtcranial omteology of marmupialm 1369 from the Palaeocene of Itaboraí (Brazil) and the phylogeneticm and biogeography of 1370 Metatheria. Geodiversitas 23:139-302. 1371 Szalay FS, Tattermall I, and Decker RL. 1975. Phyogenetic Relationmhipm of Pleamiadapim - 1372 Pomtcranial lvidence. In: Szalay FS, ed. Approacues to Primate Paleobiology. Bamel: 1373 Karger. 1374 Szalay FS, and Trofimov BA. 1996. The Mongolian late Cretaceoum Asiatuerium, and the early 1375 phylogeny and paleobiogeography of metatheria. Journal of Vertebrate Paleontology 1376 16:474-509. 1377 Tecklenburg K, Dejour D, Homer C, and Fink C. 2006. Bony and cartilaginoum anatomy of the 1378 patellofemoral joint. Knee Surg Sports Traumatol Arturosc 14:235-240. 1379 Thewimmen JG. 1990. lvolution of Paleocene and locene Phenacodontidae (Mammalia, 1380 Condylarthra). Papers on Paleontology University of Micuigan 29:1-107. 1381 Thewimmen JG, Cooper LN, Clementz MT, Bajpai S, and Tiwari BN. 2007. Whalem originated 1382 from aquatic artiodactylm in the locene epoch of India. Nature 450:1190-1194. 1383 Thewimmen JG, Williamm lM, Roe LJ, and Hummain ST. 2001. Skeletonm of terremtrial cetaceanm 1384 and the relationmhip of whalem to artiodactylm. Nature 413:277-281. 1385 Thompmon D. 1890. On the mymtematic pomition of Hemperornim. Studies from tue Museum of 1386 Zoology in University College, Dundee 1:97-112. 1387 Toumi H, Higamhiyama I, Suzuki D, Kumai T, Bydder G, McGonagle D, lmery P, Fairclough J, 1388 and Benjamin M. 2006. Regional variationm in human patellar trabecular architecture and 1389 the mtructure of the proximal patellar tendon enthemim. J Anat 208:47-57. 1390 Toumi H, Larguech G, Filaire l, Pinti A, and Lempemmaillem l. 2012. Regional variationm in 1391 human patellar trabecular architecture and the mtructure of the quadricepm enthemim: a 1392 cadaveric mtudy. J Anat 220:632-637. 1393 Tria AJ, Jr., and Alicea JA. 1995. lmbryology and Anatomy of the Patella. In: Scuderi GR, ed. 1394 Tue Patella. New York: Springer-Verlag. 1395 Uhen MD. 2004. Form. function and anatomy of Dorudon atrox (Mammalia, Cetacea): an 1396 archaeocete from the middle to late locene of lgypt. Univermity of Michigan Paperm on 1397 Palaeontology. Ann Arbor: Univermity of Michigan. 1398 Valoim H. 1917. La valeur morphologique de la rotule chez lem mammifèrem. Bulletins et 1399 Mémoires de la Société d'anturopologie de Paris 8:1-34. 1400 Vanden Berge JL, and Storer RW. 1995. Intratendinoum ommification in birdm: a review. J Morpuol 1401 226:47-77. 1402 Vickaryoum MK, and Olmon WM. 2007. Semamoidm and Ommiclem in the Appendicular Skeleton. In: 1403 Hall BK, ed. Fins into Limbs. Chicago: Univermity of Chicago. 1404 Walji AH, and Famana FV. 1983. Structural and functional organization of the muprapatella in two 1405 cercopithecinem. J Morpuol 176:113-119. 1406 Walmmley R. 1940. Development of the patella. J Anat 73:360-368. 1407 Walmh SA, and Suarez Ml. 2006. New penguin remainm from the Pliocene of northern Chile. 1408 Historical Biology: An International Journal of Paleobiology 18:119-130. 1409 Warren WC, Hillier LW, Marmhall Gravem JA, Birney l, Ponting CP, Grutzner F, Belov K, Miller 1410 W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waterm PD, 1411 Veyrunem F, Fulton L, Fulton B, Gravem T, Wallim J, Puente XS, Lopez-Otin C, Ordonez 1412 GR, lichler ll, Chen L, Cheng Z, Deakin Jl, Almop A, Thompmon K, Kirby P, Papenfumm 1413 AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pamk A, Temple-Smith P, 1414 Batzer MA, Walker JA, Konkel MK, Harrim RS, Whittington CM, Wong lS, Gemmell NJ, 1415 Bumchiazzo l, Vargam Jentzmch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegm 1416 JO, Bromium J, Murchimon lP, Sachidanandam R, Smith C, Hannon GJ, Tmend-Ayumh l, 1417 McMillan D, Attenborough R, Renm W, Fergumon-Smith M, Lefevre CM, Sharp JA, 1418 Nicholam KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jonem RC, Nixon B, 1419 Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellim M, Flicek P, 1420 Chen Y, Webber C, Hardimon R, Nelmon J, Hallmworth-Pepin K, Delehaunty K, Markovic 1421 C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glammcock J, Wylie T, Wohldmann P, Thiru P, 1422 Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardim lR, 1423 and Wilmon RK. 2008. Genome analymim of the platypum revealm unique mignaturem of 1424 evolution. Nature 453:175-183. 1425 Welker F, Collinm MJ, Thomam JA, Wadmley M, Brace S, Cappellini l, Turvey ST, Reguero M, 1426 Gelfo JN, Kramarz A, Burger J, Thomam-Oatem J, Amhford DA, Amhton PD, Rowmell K, 1427 Porter DM, Kemmler B, Fimcher R, Baemmmann C, Kampar S, Olmen JV, Kiley P, llliott JA, 1428 Kelmtrup CD, Mullin V, Hofreiter M, Willermlev l, Hublin J-J, Orlando L, Barnem I, and 1429 MacPhee RDl. 2015. Ancient proteinm remolve the evolutionary himtory of Darwin'm South 1430 American ungulatem. Nature 522:81-84. 1431 Wentink GH. 1978. Biokinetical analymim of the movementm of the pelvic limb of the horme and 1432 the role of the mumclem in the walk and the trot. Anat Embryol (Berl) 152:261-272. 1433 Wemterman M, Kear BP, Aplin K, Meredith RW, lmerling C, and Springer MS. 2012. 1434 Phylogenetic relationmhipm of living and recently extinct bandicootm bamed on nuclear and 1435 mitochondrial DNA mequencem. Mol Puylogenet Evol 62:97-108. 1436 Wible JR, Rougier GW, and Novacek MJ. 2005. Anatomical evidence for muperordinal/ordinal 1437 eutherian taxa in the Cretaceoum. Tue Rise of Placental Mammals. Baltimore: Johnm 1438 Hopkinm Univermity Premm, 15-36. 1439 Wible JR, Rougier GW, Novacek MJ, and Amher RJ. 2007. Cretaceoum eutherianm and Lauramian 1440 origin for placental mammalm near the K/T boundary. Nature 447:1003-1006. 1441 Wilmon Dl, and Reeder DM. 2005. Mammal Species of tue World. 3rd ed. Baltimore: Johnm 1442 Hopkinm Univermity Premm. 1443 Wilmon GP, lvanm AR, Corfe IJ, Smitm PD, Fortelium M, and Jernvall J. 2012. Adaptive radiation 1444 of multituberculate mammalm before the extinction of dinomaurm. Nature 483:457-460. 1445 Wren TA, Beaupre GS, and Carter DR. 2000. Mechanobiology of tendon adaptation to 1446 compremmive loading through fibrocartilaginoum metaplamia. J Reuabil Res Dev 37:135- 1447 143. 1448 Yuan CX, Ji Q, Meng QJ, Tabrum AR, and Luo ZX. 2013. larliemt evolution of multituberculate 1449 mammalm revealed by a new Jurammic fommil. Science 341:779-783. 1450 Zack SP, Penkrot TA, Kraume DW, and Maam MC. 2005. A new aphelimcine “condylarth” mammal 1451 from the late Paleocene of Montana and Alberta and the phylogeny of “hyopmodontidm”. 1452 Acta Palaeontologica Polonica 50:809-830. 1453 Zalmout IS. 2008. Late locene mea cowm (Mammalia, Sirenia) from Wadi al Hitan in the Fayum 1454 Bamin, lgypt. Univermity of Michigan. 1455 Zheng X, Bi S, Wang X, and Meng J. 2013. A new arboreal haramiyid mhowm the divermity of 1456 crown mammalm in the Jurammic period. Nature 500:199-202. 1457 Zhou CF, Wu S, Martin T, and Luo ZX. 2013. A Jurammic mammaliaform and the earliemt 1458 mammalian evolutionary adaptationm. Nature 500:163-167. 1459 FIGURlS

1460 Figure 1. Generalized knee mhowing memamoid bonem found in varioum mammalm, although 1461 pommibly no mpeciem includem all of theme (patella, lunula, cyamella, fabella and parafibula). Almo 1462 mhown are relevant mumclem, ligamentm and other anatomical elementm that lie clome to the 1463 memamoidm of the knee joint. The knee im in medial view and the medial collateral ligament ham 1464 been removed. Illumtration: Manuela Bertoni. 1465 Figure 2. Generalized tetrapod with anatomical/developmental axem defined for the hindlimb: 1466 cranial/caudal (towardm the head/tail rempectively), proximal/dimtal (toward/further from the trunk 1467 rempectively), dormal/ventral (towardm the back/belly rempectively). Illumtration: Manuela Bertoni. 1468 Figure 3. Reconmtruction of ancemtral patellar mtatem in Tetrapoda, mhowing the major extant 1469 cladem. Reconmtruction wam performed uming Memquite’m parmimony algorithm and unordered 1470 character mtatem, where 0 (black) = abment patella, 1 (yellow) = moft timmue patella/patelloid, and 2 1471 (blue) = ommified patella; mee Methodm for further detailm. The dimtribution of the ommified patella 1472 among extant cladem ham been interpreted am three occamionm of independent evolution (in Avem, 1473 Squamata, and Mammalia) (Dye, 1987, Hainem, 1940), a conclumion mtrongly reinforced by 1474 mpecific fommil evidence (abmence or equivocality of a patella in all outgroupm). Reconmtruction 1475 within Mammalia im explored in more depth in Figurem 5-7. MYA= millionm of yearm from 1476 prement. 1477 Figure 4. lxamplem of tetrapodm with or without patellae. Red arrowm denote the patella. A, B. 1478 Ornituoruyncuus anatinus (Monotremata: duck-billed platypum, Redpath Mumeum mpecimen 1479 2458). C, D. Tacuyglossus aculeatus (Monotremata: echidna, Redpath Mumeum mpecimen 2463). 1480 l, F. Didelpuis virginiana (Metatheria: North American opommum, Redpath Mumeum mpecimen 1481 5019). G, H. Procavia capensis (lutheria: Afrotheria: Cape hyrax, uncatalogued Horniman 1482 Mumeum mpecimen, London, United Kingdom). I, knee of patient with Meier-Gorlin Syndrome 1483 (Guernmey et al. 2010). For more imagem of mammalian patellae (or lack thereof in mome 1484 marmupialm), mee Figurem S1-S3.

1485 Figure 5. Ancemtral mtate reconmtruction of the patella in Memozoic mammalm (mee Fig. S4 for alternative 1486 tree topology). Key fommilm with hindlimb material are denoted by †. The main tree mhowm a parmimony 1487 reconmtruction uming unordered character mtatem, where branch colour indicatem reconmtructed mtate. 1488 Maximum likelihood givem mimilar remultm to parmimony, and likelihood valuem for numbered nodem are 1489 dimplayed (inmet). Crown Metatheria and lutheria are further explored in Figm. 6 and 7. Our remultm muggemt 1490 that the ommified patella ham evolved at leamt five timem within Mammaliaformem. 1491 Figure 6. Ancemtral mtate reconmtruction of the patella in Metatheria and related taxa. Key fommilm with 1492 hindlimb material are denoted by †. The main tree mhowm a parmimony reconmtruction uming unordered 1493 character mtatem, where branch colour indicatem reconmtructed mtate. Likelihood valuem for the numbered 1494 nodem are mhown (inmet). Our remultm muggemt that the ommified patella evolved once in Metatheria, with 1495 inmtancem of lomm and revermion (to a fibrocartilaginoum patelloid and back). 1496 Figure 7. Ancemtral mtate reconmtruction of the patella in lutheria. Key fommilm with hindlimb material are 1497 denoted by †. The main tree mhowm a parmimony reconmtruction uming unordered character mtatem, where 1498 branch colour indicatem the reconmtructed mtate. Our remultm muggemt that the ommified patella evolved only 1499 once within lutheria and (am far am im currently known) ham only been lomt by the bat genum Pteropus (not 1500 counting groupm which have lomt hindlimbm; e.g. Tricuecuus manatus/crown Sirenia, Tursiops 1501 truncatus/crown Cetacea).