Evolutionary structure and timing of major habitat shifts in Crocodylomorpha

Extant crocodylomorphs are semiaquatic ambush predators largely restricted to freshwater or estuarine environments, but the group is ancestrally terrestrial and inhabited a variety of ecosystems in the past. Despite its rich ecological history, little effort has focused on elucidating the historical pattern of ecological transitions in the group. Traditional views suggested a single shift from terrestrial to aquatic in the Early Jurassic. However, new fossil discoveries and phylogenetic analyses tend to imply a multiple-shift model. Here we estimate ancestral habitats across a comprehensive phylogeny and show at least three independent shifts from terrestrial to aquatic and numerous other habitat transitions. Neosuchians first invade freshwater habitats in the Jurassic, with up to four subsequent shifts into the marine realm. Thalattosuchians first appear in marine habitats in the Early Jurassic. Freshwater semiaquatic mahajangasuchids are derived from otherwise terrestrial notosuchians. Within nearly all marine groups, some species return to freshwater environments. Only twice have crocodylomorphs reverted from aquatic to terrestrial habitats, both within the crown group. All living non-alligatorid crocodylians have a keratinised tongue with salt-excreting glands, but the lack of osteological correlates for these adaptations complicates pinpointing their evolutionary origin or loss. Based on the pattern of transitions to the marine realm, our analysis suggests at least four independent origins of saltwater tolerance in Crocodylomorpha.


I) PRIMARY ANALYSIS -Ancestral state reconstruction likelihoods II)
SENSITIVITY ANALYSES -Ancestral state reconstruction likelihoods a. Calsoyasuchus as goniopholidid b. Stolokrosuchus as basal neosuchian c. Thalattosuchia as sister to Mesoeucrocodylia d. Thalattosuchia as sister to Tethysuchia ("longirostrine clade") e. Gavialis and Tomistoma as living sister taxa (including thoracosaurs) f. Gavialis and Tomistoma as living sister taxa (excluding thoracosaurs) III) Stratigraphic ranges for study taxa IV) Material and references used for phylogenetic character scoring V) Character list and state descriptions of the data matrix used in the phylogenetic analysis VI) Supplemental References

V) Character list and state descriptions of the data matrix used in the phylogenetic analysis
Characters are arranged by anatomical region. The character list was assembled from numerous sources. Many of the characters have been reworded or modified from their original source. The original publication from which the character was taken is listed in the right column. The original character number is in parentheses. Characters treated as additive for the ordered-character analysis are denoted by "ORDERED" following the character description. Characters new to this analysis denoted by "NEW". Notes on applicability or other comments follow the description in italics.

Char. Number
Character description Original publication 1.
Sculpture of external surface of rostrum: 0: absent or very reduced (slight grooves) 1: present as deep pits or grooves Gasparini et al. 2006 (252) 2. Rostral proportions at orbits: 0: rostrum narrows gradually anterior to orbits 1: rostrum narrows abruptly at orbits as in Gavialis gangeticus; Protosuchus richardsoni Clark 1994 (2) 3. Rostral length measured from anterior orbital edge to anterior contour of rostrum: 0: equal to or longer than remainder of skull as measured to the posterior end of the quadrate 1: shorter than remainder of skull Ortega et al. 2000 (3) 4. Rostral length measured from anterior orbital edge to anterior contour of rostrum: 0: equal to or slightly longer than distance from anterior orbital edge to posterior parietal contour 1: at least twice the distance from anterior orbital edge to posterior parietal contour Ortega et al. 2000 (4) 5.
Orientation of external naris: 0: anteriorly or anterolaterally directed 1: dorsally or anterodorsally, located at anterior tip of snout, Clark 1994 (6) with little or no premaxilla visible at anterior margin (or perinarial fossa extends to anterior margin of premaxilla as in Steneosaurus bollensis) 2: dorsally, located posterior to anterior tip of snout, with premaxilla broadly visible anterior to naris 8.
Premaxillo-maxillary suture direction in palatal view (direction of suture is evaluated with respect to a theoretical line that passes between the lateral contact of both bones): 0: anteriorly directed 1: sinusoidal, posteromedially directed on its lateral half and Ortega et al. 2000 (9) anteromedially directed along its medial region 2: posteriorly directed 3: perpendicular to the longitudinal axis of the skull 18.
Ventrally opening notch at premaxilla/maxilla contact for acceptance of enlarged dentary tooth (or teeth): 0: absent, snout not constricted at premaxilla/maxilla contact 1: present as a laterally open notch, snout constricted at premaxilla/maxilla contact as in Crocodylus niloticus 2: snout broad at contact with premaxilla and maxilla with notch opening dorsally as a large foramen as in Dibothrosuchus Clark 1994 (9) 20.  Pol, 1999 (152) 24.
Position of anterior portion of maxillary tooth row in relation to dentary tooth row: 0: adjacent to 1: offset labially and ventrally as in Comahuesuchus Sereno et al. 2003 (75) 25.
Nasal orientation at posterior border: 0: nasals converge at sagittal plane posteriorly 1: nasals separated posteriorly by an anterior sagittal projection of frontal Ortega et al. 2000 (24) 35. Distance between the posterior processes of nasals relative to the distance from the posterior process of the nasal to the anterior margin of the supratemporal fossa (inapplicable in taxa lacking an anterior process of frontal separating the nasals posteriorly): 0: much shorter 1: nearly as long Jouve 2009  (312) 36. Nasal bones: 0: paired 1: partially or completely fused as in Dyrosaurus phosphaticus Gasparini et al. 2006 (257) 37. Maximal width of the nasals relative to the minimal width of the snout in dorsal view: 0: narrower than or nearly as wide 1: wider than 2: more than twice as wide 49. Prefrontal anterior process: 0: two anterior processes, one anterodorsal and one anteroventral, separated by posterodorsal process of lacrimal 1: single short anterior process (shorter than or as long as the orbit) 2: single long anterior process (longer than the orbit) Gomani 1997 (4) 50.