Genetics/Crocodilia

Crocodilia (or Crocodylia) is an order of mostly large, predatory, semiaquatic reptiles, known as crocodilians. They are the closest living relatives of birds, as the two groups are the only known survivors of the Archosauria. The order Crocodilia includes the true crocodiles (family Crocodylidae), the alligators and caimans (family Alligatoridae), and the gharial and false gharial (family Gavialidae). Although the term 'crocodiles' is sometimes used to refer to all of these, crocodilians is a less ambiguous vernacular term for members of this group.

Brørup interstadial
The "Brørup interstade [is about] 100 ka BP". It corresponds to GIS 23/24.

MIS Boundary 5.4 (peak) is at 109 ka.

"The Aldabra Limestone is a marine unit deposited between 118 and 163 Ka, at a time when Aldabra Atoll was completely submerged (Braithwaite et al., 1973; Arnold, 1976; Taylor et al., 1979). Crocodiles presumably did not live there at that time. Crocodile remains are known from Aldabran deposits older than 120,000 years, but these are isolated teeth with limited taxonomic value, and pre-submergence populations were presumably extirpated when the atoll was submerged. Aldabrachampsus is from cavity fills younger than 118 Ka (Arnold, 1976)."

"Known fossil localities elsewhere in the western Indian Ocean are no older than 25 Ka [Letzteiszeitliches Maximum] (Burney et al., 2004), and the only known crocodiles are "C." robustus or Crocodylus sensu stricto (Gerlach and Canning, 1993). These localities may post-date the extinction of Aldabrachampsus dilophus."

Eemian interglacial
The "controversially split Eemian period, the predecessor of our own warm period about 125,000 years ago."

"The Eem interglaciation […] lasted from 131 to 117 kyr B.P."

Voay is an extinct genus of crocodile from Madagascar and includes only one species—V. robustus which may have disappeared in the extinction event that wiped out much of the endemic megafauna such as the elephant bird following the arrival of humans to Madagascar around 2000 years ago.

It has recently been proposed that the Nile crocodile only migrated to the island from mainland Africa after V. robustus had become extinct in Madagascar.

When V. robustus was first described in 1872, it was originally assigned to the genus Crocodylus. It was later found to morphologically have had more in common with the extant Osteolaemus, or dwarf crocodile, than Crocodylus, which included a depressed pterygoid surface that forms a choanal "neck" on the palate. In contrast to the morphological similarities with Osteolaemus, a 2021 study using paleogenomics found Voay to be a sister group to Crocodylus, with both genera diverging in the mid-late Oligocene; this indicates that the apparent similarities with Osteolaemus are likely due to convergent evolution.

Calabrian
The magnetic field reversal to the present geomagnetic poles (Jaramillo subchron) occurred at 1,060,000 yr BP.

"The [Calabrian] GSSP occurs at the base of the marine claystone conformably overlying sapropelic bed ‘e’ within Segment B in the Vrica section. This lithological level represents the primary marker for the recognition of the boundary, and is assigned an astronomical age of 1.80 Ma on the basis of sapropel calibration."

"The boundary falls between the highest occurrence of Discoaster brouweri (below) and the lowest common occurrence of left-coiling Neogloboquadrina pachyderma (above), and below the lowest occurrences of medium-sized Gephyrocapsa (including G. oceanica) and Globigerinoides tenellus."

In the image on the right, the Vrica section includes specifically the GSSP of the Calabrian Stage fixed at the top of layer 'e'.

Gelasian
Crocodylus anthropophagus is an extinct species of crocodile from the Pleistocene of Tanzania. It lived 1.84 million years ago. It was a large-sized predator reaching a length of 5 m.

Crocodylus anthropophagus was first named by Christopher A. Brochu, Jackson Njau, Robert J. Blumenschine and Llewellyn D. Densmore in 2010. The specific name anthropophagus is from Greek word "anthropos" that means "human" and Greek word "phagos" that means "eater", in reference to the evidence that this animal included hominids in its diet.

Crocodylus anthropophagus was the largest predator encountered by human ancestors at Olduvai Gorge, as indicated by hominin specimens preserving crocodile bite marks from these sites. Its type locality is near those for Homo habilis and Paranthropus boisei.

MIS Boundary 69/70 is at 1859.5 ka.

MIS Boundary 68/69 is at 1849 ka.

MIS Boundary 67/68 is at 1832.5 ka.

"The base of the Quaternary System [shown in the image above] is defined by the Global Stratotype Section and Point (GSSP) of the Gelasian Stage at Monte San Nicola in Sicily, Italy, currently dated at 2.58 Ma."

"The astrochronological age of sapropel MPRS 250 (mid-point), corresponding to precessional cycle 250 from the present, is 2.588 Ma (Lourens et al., 1996), which can be assumed as the age of the boundary."

Piacenzian
"The base of the beige marl bed of the small-scale carbonate cycle 77 (sensu Hilgen, 1991b) is the approved base of the Piacenzian Stage (that is the Lower Pliocene-Middle Pliocene boundary). It corresponds to precessional excursion 347 as numbered from the present with an astrochronological age estimate of 3.600 Ma (Lourens et al., 1996a)."

Zanclean
Fossil remains of a saltwater crocodile excavated from the Allingham Formation in northern Queensland were dated to the Pliocene.

The Allingham Formation is a lake and stream deposit within the Nulla Basalt Province, containing the fossils which the Bluff Downs Local Fauna are attributed to. It consists of a mixture of sediment that originated on land and was washed away after eroding into nearby waterbodies (terrigenous sediment), clays, silts, sands (including calcareous sands), and Chara limestones (calcareous nodules that were deposited directly over the fossiliferous sediment and consequently overlain by basalt). These sediments were formed in lakes and rivers (i.e. are lacustrine and fluviatile), indicating the presence of various water bodies such as lakes, rivers and streams in the palaeoenvironment at the time of deposition. There were several different depositional events and analysis of the sediments suggests that during the early Pliocene, a stream widened to form a shallow lake. The formation could be as young as 4.0 to 3.6 million years old, with the fossils were likely deposited at the lower end of the period between 5.2 and 3.6 million years ago.

Crocodylus thorbjarnarsoni is an extinct species of Crocodylus from the Pliocene and Pleistocene of the Turkana Basin in Kenya. It is closely related to the species Crocodylus anthropophagus, which lived during the same time in Tanzania. C. thorbjarnarsoni could be the largest known true crocodile, with the largest skull found indicating a possible total length up to 7.6 m. It may have been a predator of early hominins. Crocodylus thorbjarnarsoni was named by Christopher Brochu and Glenn Storrs in 2012 in honor of John Thorbjarnarson, a conservationist who worked to protect endangered crocodilians.

Crocodylus thorbjarnarsoni is distinguished from other crocodiles by its broad snout. It has small raised rims on the prefrontal bones in front of the eyes, a feature also seen in some Nile crocodile individuals. The squamosal bones form raised rims along the sides of the skull table, similar to the crests in C. anthropophagus but much smaller. Also like C. anthropophagus, it has nostrils that open slightly forward rather than directly upward.

The largest C. thorbjarnarsoni skull found (KNM-ER 1682) measures 85 cm from the tip of the snout to the back of the skull table, in comparison, the largest known extant Crocodylus skull is that of a saltwater crocodile, measuring 76 cm. Based on regression analysis for Crocodylus, this corresponds to a total length of 6.2 - 6.5 m but such analysis have been shown to underestimate the size of very large individuals by as much as 20%, which means it could have been as long as 7.6 m.

Crocodylus thorbjarnarsoni likely preyed on human ancestors like Paranthropus and early members of the genus Homo, both of which are known from the Turkana Basin. Direct evidence of crocodilian predation is known from bite marks on hominin bones from the Olduvai Gorge, and these marks were likely made by the closely related crocodile C. anthropophagus (anthropophagus means "human eater" in Greek). No hominin bones from the Turkana Basin bear crocodilian bite marks, so there is no direct evidence that C. thorbjarnarsoni preyed on hominins. However, modern Nile crocodiles are known to consume adult humans, and since C. thorbjarnarsoni was larger than any Nile crocodile, it easily could have eaten smaller-bodied human ancestors. Brochu and Storrs hypothesized that the lack of bite marks could have been due to hominin's awareness of crocodiles and ability to evade them, explaining that "this conflict—eat and drink, but maybe die—was presumably foremost amongst the concerns our predecessors felt when approaching ancient waterways inhabited by Crocodylus thorbjarnarsoni." Another explanation was that C. thorbjarnarsoni may have eaten hominins whole with little need for biting, since it was much larger.

Crocodylus thorbjarnarsoni is known from nine skulls, all of which are housed in the National Museum of Kenya. The holotype is a nearly complete skull and lower jaw called KNM-ER 1683 and comes from the approximately 2-million-year-old Koobi Fora Formation on the eastern shore of Lake Turkana. The skulls KNM-ER 1681 and KNM-ER 1682 have also been found from the formation. Three other skulls are known from the Nachukui Formation, west of the holotype's locality. KNM-WT 38977 is from the 2.5- to 3.4-million-year-old Lower Lomekwi Member, KNM-LT 26305 is from the 3.9-million-year-old Kaiyumung Member, and KNM-LT 421 is from the 4.2- to 5.0-million-year-old Apak Member. Three additional skulls called KNM-KP 18338, KNM-KP 30604, and KNM-KP 30619 are known from the southern Turkana Basin in the Kanapoi Formation, dating between 4.07 and 4.12 million years. KNM-ER 1682, KNM-LT 421, KNM-LT 26305, and KNM-KP 30619 were previously assigned to Rimasuchus lloydi, and their reassignment to C. thorbjarnarsoni reduces the range of R. lloydi to Northern Africa.

Tip dating study simultaneously using morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data established the inter-relationships within Crocodylidae. In 2021, using paleogenomics, extracting DNA from the extinct Voay, better established the relationships within Crocodylidae, including the subfamilies Crocodylinae and Osteolaeminae.

"All of Pliocene time, without a gap, is physically represented in the three stages of which it is composed, in a single demonstrably uninterrupted sequence of highly fossiliferous Upper Cenozoic deep-water strata on the southern coast of Sicily. From bottom to top, the Pliocene consists of the Lower Pliocene Zanclean Stage, with a boundary-stratotype at Eraclea Minoa and a unit-stratotype at Capo Rossello; the Middle Pliocene Piacenzian Stage, defined at Punta Piccola (Castradori et al., 1998); and the Upper Pliocene Gelasian Stage, defined at Monte San Nicola near Gela (Rio et al., 1994, 1998) [...]."

"The boundary-stratotype of the stage is located in the Eraclea Minoa section on the southern coast of Sicily (Italy), at the base of the Trubi Formation. The age of the Zanclean and Pliocene GSSP at the base of the stage is 5.33 Ma in the orbitally calibrated time scale, and lies within the lowermost reversed episode of the Gilbert Chron (C3n.4r), below the Thvera normal subchron."

Messinian
The Messinian is in the geologic timescale the last age or uppermost stage of the Miocene that spans the time between 7.246 ± 0.005 Ma and 5.333 ± 0.005 Ma (million years ago).

Crocodylus checchiai is an extinct species of Crocodylus from the early Pliocene of Libya and the late Miocene of Kenya, named in 1957 from the Sahabi Formation, with remains from the lower Nawata Formation in the Turkana Basin of Kenya that were first attributed to the Nile crocodile now have been reassigned to C. checchiai, extending its geographic and temporal range.

Serravallian
The top of the Serravallian (the base of the Tortonian stage) is at the last common appearance of calcareous nannoplanktons Discoaster kugleri and planktonic foram Globigerinoides subquadratus. It is also associated with the short normal-polarized chronozone C5r.2n.

"The oldest undisputed fossils of the genus are of Middle Miocene age, with the oldest species, Crocodylus palaeindicus, being found on and near the Indian subcontinent, suggesting that the genus might have originated in that region (Scheyer et al., 2013)."

The Serravallian is in the middle Miocene and spans the time between 13.82 Ma and 11.63 Ma (million years ago), follows the Langhian and is followed by the Tortonian.

The base of the Serravallian is at the first occurrence of fossils of the nanoplankton species Sphenolithus heteromorphus and is located in the chronozone C5ABr. The official Global Boundary Stratotype Section and Point (GSSP) for the Serravallian is in the 'Ras il-Pellegrin' section, located at the 'Ras il-Pellegrin' headland in the vicinity of 'Fomm ir-Rih' Bay, SW Malta. The base of the Serravallian is represented in the field as the formation boundary between the Globigerina Limestone formation and the Blue Clay formation. The base of the Serravallian is related to the Mi3b oxygen isotope excursion marking the onset of the Middle Miocene Cooling step.

Middle Eocene
The Crocodylomorpha of the Messel Formation are represented by Pristichampsus rollinatii and Bergisuchus dietrichbergi, which were most likely land dwellers. In contrast, the diplocynodontins Diplocynodon darwini and Baryphracta deponiae, which are related to the alligators and caimans, the alligators Hassiacosuchus Haupti (formerly Allognathosuchus Haupti) and Allognathosuchus gracilis as well as the Asiatosuchus germanicus, which is related to the real crocodiles, lived mainly in the water.

Lutetian
The Lutetian began 47.8 Ma and ended 41.2 Ma.

The only robust occurrence of Brachyuranochampsa is B. eversolei from the middle Eocene of Wyoming.

Ypresian
The Ypresian began 56.0 Ma and ended 47.8 Ma.

The species, Brachyuranochampsa zangerli from the lower Bridger Formation at Grizzly Buttes, has been synonymized with another primitive crocodilian, "Crocodylus" affinis, also known from the Bridger Formation

Range of "Crocodylus" affinis is from 50.3 Ma to 47.8 Ma.

"Crocodylus" affinis is an extinct species of crocodyloid from the lower Bridger Formation discovered in 1871, described along with every other species of crocodyloid in the Bridger Formation, under the genus Crocodylus. The known specimen of "Crocodylus" affinis is a skull found at Grizzly Buttes, Wyoming, measuring 13 inches in length on the upper surface. Phylogenetic studies of crocodyloids show that ''"C." affinis is not a species of Crocodylus'', but a genus has not yet been erected to include the species. Other Bridger species such as Crocodylus clavis and Brachyuranochampsa zangerli have been synonymized with ''"C." affinis''.

"Crocodylus" acer is an extinct species of crocodyloid from the early Eocene of Utah from a single well preserved skull described in 1882, found from the Wasatchian-age Green River Formation, with a long, narrow snout and a low, flattened skull.

Some postcranial bones have been attributed to ''"C." acer but they have more recently been suggested to belong to the related species "C." affinis''. Although they were first placed in the genus Crocodylus, ''"C." acer and "C." affinis are not crocodiles, but as early members of Crocodyloidea, only distantly related to Crocodylus''. Although it represents a distinct genus, a generic name has not yet been proposed for ''"C." acer''.

Tip dating simultaneously using morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data established the inter-relationships within Crocodilia, which was expanded upon using paleogenomics by extracting DNA from the extinct Voay.

Maastrichtian
Prodiplocynodon is the only crocodyloid known from the Cretaceous and existed during the Maastrichtian stage. The only species of Prodiplocynodon is the type species P. langi from the Lance Formation of Wyoming, known only from a single holotype skull lacking the lower jaw.

Simultaneously using morphological, molecular (DNA sequencing), and stratigraphic (fossil age) data established the inter-relationships within Crocodilia, which was expanded upon in 2021 using paleogenomics by extracting DNA from the extinct Voay.

The below cladogram shows the results of the latest studies, which placed Prodiplocynodon outside of Crocodyloidea, as more basal phylogenetics than Longirostres (the combined group of crocodiles and gavialids).

Cenomanian
Crocodilia first appeared 95 million years ago in the Cenomanian.

The Cenomanian per the International Commission on Stratigraphy is the oldest or earliest age of the Late Cretaceous or the lowest stratigraphic stage of the Upper Cretaceous.

As a unit of geologic time measure, the Cenomanian age spans the time between 100.5 ± 0.9 Ma and 93.9 ± 0.8 Ma, preceded by the Albian and is followed by the Turonian, where the Upper Cenomanian starts approximately at 95 Ma.

The base of the Cenomanian is placed at the first appearance of foram species Rotalipora globotruncanoides in the stratigraphic record, located in an outcrop at the western flank of Mont Risou, near the village of Rosans in the French Alps (département Hautes-Alpes, coordinates: 44°23'33"N, 5°30'43"E), in the reference profile, located 36 meters below the top of the Marnes Bleues Formation.

Toarcian


"The genus Mystriosaurus, established by Kaup in 1834, was one of the first thalattosuchian genera to be named. The holotype, an incomplete skull from the lower Toarcian Posidonienschiefer Formation of Altdorf (Bavaria, southern Germany), is poorly known with a convoluted taxonomic history. For the past 60 years, Mystriosaurus has been considered a subjective junior synonym of Steneosaurus. However, our reassessment of the Mystriosaurus laurillardi holotype demonstrates that it is a distinct and valid taxon. Moreover, we find the holotype of “Steneosaurus” brevior, an almost complete skull from the lower Toarcian Whitby Mudstone Formation of Whitby (Yorkshire, UK), to be a subjective junior synonym of M. laurillardi. Mystriosaurus is diagnosed in having: a heavily and extensively ornamented skull; large and numerous neurovascular foramina on the premaxillae, maxillae and dentaries; anteriorly oriented external nares; and four teeth per premaxilla. Our phylogenetic analyses reveal M. laurillardi to be distantly related to Steneosaurus bollensis, supporting our contention that they are different taxa. Interestingly, our analyses hint that Mystriosaurus may be more closely related to the Chinese teleosauroid (previously known as Peipehsuchus) than any European form."

"A prehistoric crocodile [Mystriosaurus laurillardi] that lived 180 million years ago has finally been identified – nearly 250 years after its fossil was unearthed in Germany."

Second down on the right is a photograph "of teleosauroid thalattosuchian specimen (UH 7), lower Toracian of Holzmaden (southwestern Germany), which was described by Mueller-Töwe (2006) as “Steneosaurus” brevior Blake, 1876, and which we herein refer to tentatively as ?Mystriosaurus sp."

Hettangian
"Since the 1960’s, the LO (lowest occurrence) of the ammonite Psiloceras (usually the species P. planorbis [first image on the right]) has provided the working definition of the TJB (e.g., Lloyd, 1964; Maubeuge, 1964; Cope et al., 1980; Warrington et al., 1994; Gradstein et al., 2004)."

The "beds immediately above the Chinle formation contain dinosaur tracks, several skeletons of America's earliest crocodile, Protosuchus richardsoni Brown, and dinosaur skeletons. Our only means of dating the rocks is through these fossil vertebrates (some invertebrates are known but are not conclusive). The dinosaur tracks are tridactyl and bipedal, and those in the section measure 23 cm from heel to tip of third toe and have a pace of about 1 meter. C. L. Camp and the writer have also seen such tracks near Zion Canyon, at Pipe Springs, Kanab, and Kayenta in rocks of similar lithology and presumably equivalent age. Gregory (1917, p. 56) collected similar tracks from Navajo Canyon (1917, PI. 9 C) and Willow Springs. These were submitted to Lull who compared them with tracks from the Connecticut Valley and concluded (Gregory, 1917, p. 56), on size alone, that the Kayenta tracks were younger. Baker (1946, p. 67) found similar tracks in "the transition zone between the Kayenta and Navajo in rocks that were mapped as Navajo but might equally well have been considered Kayenta." His locality was on Iron Wash near the San Rafael Swell. The tracks were examined by Gilmore who evidently made no comment on their age."

"The careful study of Protosuchus by Colbert and Mook (1951) showed that it is of little stratigraphic importance and could be either Triassic or Jurassic. The preliminary study of the dinosaur places it in the Early or Early Middle Jurassic. Evidence to date thus indicates that in this region the Chinle formation is Upper Triassic and the Kayenta formation Lower or Middle Jurassic."

"The Global Stratotype Section and Point (GSSP) defining the base of the Jurassic System Lower Jurassic Epoch and Hettangian Stage is situated at the Kuhjoch pass, Karwendel Mountains, Northern Calcareous Alps, Austria (47°29'02"N/11°31'50"E). The Triassic-Jurassic (T-J) boundary is exposed at Kuhjoch West and at Kuhjoch East [in the second image on the right], and corresponds to the first occurrence (FO) of the ammonite Psiloceras spelae tirolicum [at the top of this section]."

Another FO is that of "the aragonitic foraminifer Praegubkinella turgescens"

The Triassic/Jurassic boundary occurs at 205.7±4.0 Ma (million years ago).

Gangetian
The chart above indicates that the Gangetian is in the Brahmanian.

Members of the order's total group, the clade Pseudosuchia, appeared about 250 million years ago in the Early Triassic period, and diversified during the Mesozoic era.

The Permian/Triassic boundary occurs at 248.2 ± 4.8 Ma (million years ago).