Shifting faunal baselines through the Quaternary revealed by cave fossils of eastern Australia

GR1 Fig Tree Cave (AODL0253)

Fig Tree Cave (Fig. S1) has an 11 m deep entrance shaft that measures 5 × 2 m at the surface. A ledge of jammed rocks is encountered five m down, then a further six m of vertical shaft occurs before reaching a relatively flat earth and broken rock floor. From this point, phreatic passages can be followed short distances to enter the two avens (vertical shafts), each about 13 m high; both contain red flowstones and stalactites that are mostly inactive. Bone deposits are located in the soft silt under travertine at the deepest part of the cave, as well as on the wall of one passage. The total vertical depth of the cave is 18.5 m and survey passage length is 51 m.

GR2 Clunk, Clunk, Bang, Pot Cave (AODL0254)

This cave (Fig. S2) is located in a grove of fig trees 20 m from GR1. The entrance measures 2 × 1 m at the top of an 11.5 m shaft. The restricted entrance suggests that the cave has less potential to be a natural trap for large animals. Several large fig tree roots hang down the full length of the cave’s shaft and continue into the silt and broken rock floor at the bottom of the cave. The single chamber at the bottom measures just five m diameter, with little chance of extension without extensive excavation. Faunal remains were found in small niches away from the main entrance.

GR5 Ewe Beaut Cave (AODL0255)

This cave is located on grassed, gently sloping terrain (Fig. S3). There are two trees growing at the side of the 11 m vertical, solution tube entrance. The entrance measures 4 × 2 m at the surface. The cave has a high potential to act as a natural animal trap, as is obvious by the large number of bones that litter the earth and broken rock floor. A single chamber at the bottom of the shaft measures 7 × 5 m, with little chance of extension. On the western side of the chamber, a four m high section of red flowstone decorates the wall.

GR17 Red-naped Cave (AODL0256)

GR17 (Fig. S4) is located in lightly timbered and grass terrain; however, the immediate surrounds of the entrance is devoid of vegetation. The smooth bedrock around the entrance slopes abruptly into the vertical 20 m deep solution shaft. The shaft at the entrance measures 3 × 4 m and opens out to a split level single chamber, approximately nine m diameter at the bottom. The rock-pile floor slopes from west to east and ends in a dirt and rubble floor. The lowest point of Red-naped Cave contains foul air.

The most fossil-rich deposit is located in the northeast side of the main chamber. The clay deposit that contains the bones is trapped in a solution hollow dissolved from the solid bedrock approximately one m above the present sediment floor of the cave. The maximum depth of the cave is 24 m and survey length is 43 m.

GR18 Westgate Cave (AODL0257)

The two entrances to this cave are approximately one m apart under the canopy of a fig tree (Fig. S5). Both entrances are one m in diameter and either can be used to descend the 10 m pitch into a chamber below (which measures 8 × 5 m) that contains abundant speleothem formation. A six m tall tree root runs from the ceiling to the rock-fill floor. Two additional pitches of four and three m, respectively, lead to lower levels of the cave. Foul air is usually encountered beyond the first pitch. The dirt floor in the lower west section contains sheep bones and bat guano.

GR36 Lonesome Lair (AODL0258)

This small cave has little chance of being a natural animal trap (Fig. S6). Rather, it is more likely used as a residence or safe haven for animals. The entrance is located amongst fractured bedrock just above the level of the modern creek. The small gently sloping entrance passage leads to a chamber 3.5 m high by two m diameter. Several short passages of one and two m in length lead off the main chamber. Bones from wallabies and wombats were previously identified in the cave. No foul air was recorded in this cave.

GR92 Leaf Beetle (AODL0259)

GR92 has a small entrance above a vertical drop of three m to a debris floor littered with bones (Fig. S7). There is a small amount of flowstone. No foul air was recorded in this cave.

GR124 Death Trap Cave (AODL0260)

The entrance to this cave (Fig. S8) was completely closed prior to its discovery in 2010. The entrance is permanently closed with iron sheeting when not being explored. The very small entrance measures 0.8 × 0.4 m and descends vertically two m into a tight spiralling passage with several drops of about two m. A short crawl then leads into a chamber, 10 × 6 × 2 m high. A 6.5 m aven is located on the southwestern side of the chamber. To the east, a 0.6 m crawl leads to a low chamber that contains a two m tall leaning column near a five m deep, very narrow (impenetrable) rift with air flowing from below.

In the centre of the first chamber there are two holes leading to chambers below. The small chamber below this free-climb contains numerous large bones as well as an excellent example of a three m long rootsicle (tree root covered in thick calcite). From this small chamber, a low crawl passage leads to a four m climb down the side of a chamber that measures 6 × 4 × 2.7 m high, and contains an active flowstone wall.

The roof height drops to 1.2 m and a trench between adjacent fine clay banks may be followed for six m in an easterly direction. The cave height above the clay banks is just 0.2–0.3 m for a length of three m either side of the erosion trench. Several bones are visible protruding from the sediment in that part of the cave. The trench leads into a climbable passage that descends a further four m to a narrow earth floor chamber which sometimes contains foul air. This chamber also contains speleothems.

Death Trap Cave is best described as having two main levels, although there are some additional pitches on each level. The majority of the fossil bones are found in the lower level. The whole cave may be explored without ropes or ladders, however, the entrance and initial passage is tight. Death Trap Cave has a total depth of 33 m and a survey length of 90 m.

Anura

• Anura gen. et sp. Indeterminate

Frog bones were recorded as surface specimens in some caves (Table 1) including various limb bones such as tibiofibulae (AODF0907; Fig. 2A). The assemblages lack ilia, the most useful skeletal element commonly used for the taxonomic identification of frogs (Price, Tyler & Cooke, 2005). The bones are generally white in colour, unmineralised, and are most likely modern.

Scincidae

• Tiliqua scincoides

A Blue-tongue Skink is represented by a single left mandible (AODF0908; Fig. 2B) found in Death Trap Cave. It was identified on the basis of its large size, possession of a closed Meckel’s groove, and presence of large, uniform, hemispherical-conical teeth. The specimen was collected from the surface of the lower section of Death Trap Cave. It is white in colour and unmineralised, suggesting that it is modern. Blue-tongue Skinks are common in eastern Australia today.

Agamidae

• Lophognathus gilberti

Maxillae (e.g., AODF0909; Fig. 2C) and associated dentaries are referred to Gilbert’s Dragon and were recorded in three caves (Table 1). The dorsal maxillary process is constricted superiorly and broad superiorly. The suborbital margin is relatively large and the narial process is tall and robust. It possesses two pleurodont teeth of equal size and 14 acrodont teeth (seven small, seven large). They were surface specimens, slightly discoloured, and unmineralised, suggesting that they are modern. Lophognathus gilberti occurs in eastern Australia today.

Elapidae

• Elapidae gen. et sp. indet.

Several isolated vertebrae (e.g. AODF0910; Fig. 2D) and associated rib bones, as well as a near-complete desiccated skeleton of elapid (venomous) snakes were recovered as surface specimens in some of the caves (Table 1). Their identification as elapids was based on the vertebrae which possess long, acute accessory processes, and a hypapophysis that arise near the cotyle tip and extend posteriorly for approximately half the length of the condyle. The specimens are similar in size of Brown (Pseudechis australis) and Red-bellied Black snakes (Pseudechis porphyriacus), but could not be identified below the family level. The fully skeletonised specimens were found on the surface of the cave floor. The association of fragile ribs suggests that they were minimally disturbed prior to collection. They are generally white in colour and unmineralised, indicating that they are modern.

Tachyglossidae

• Tachyglossus aculeatus

There are two very different-sized species of echidna present in the caves at Glenrock. The modern Short-beaked Echidna (Tachyglossus aculeatus) is represented by a quill measuring 50 mm in length (AODF0911; Fig. 3A) from Fig Tree Cave. Echidna quills are composed of keratin, a biological material susceptible to rapid decay. The specimen is well-preserved and unmineralised, suggesting that it is modern.

• Tachyglossidae gen. et sp. indet.

A right ulna (AODF0912; Fig. 3B) and left radius (AODF0913; Fig. 3C) are referrable to a species of giant echidna. The radius (39.9 mm long) is broken close to the proximal end, just below the trochlear notch. The olecranon process has dual processes, a higher one that spreads posteromedially and a lower one that is angled anterolaterally. The anterolaterally directed process is well-developed, but is broken and missing the tip. The trochlear notch is a simple oval-shaped depression 12.3 mm across and differs from Tachyglossus by being more circular rather than ovate. The radius is also represented by the proximal end (46.1 mm long); it is clear that the bone would have been long and straight, and would have been appressed against the ulna. The head of the radius is broad and slightly cup-shaped for articulation with a bulbus condyle of the distal humerus. Both fossil specimens are substantially larger than the equivalent limbs of Tachyglossus. Two genera of giant echidna have been recognised in the Pleistocene deposits of Australia: Megalibgwilia and ‘Zaglossus’, the latter of which is likely distinct to modern Zaglossus (long-beaked echidnas of New Guinea) and also the largest-known echidna (Griffiths, Wells & Barrie, 1991). AODF0912 and AODF0913 are too fragmentary to be confidently referred to either taxon, but they are certainly not Tachyglossus. The specimens are mineralised suggesting considerable antiquity. Both specimens were found in Red-naped Cave within a deposit that contains other extinct megafaunal taxa.

Dasyuridae

• Antechinus flavipes

A right mandible (AODF0914; Fig. 4A) from GR2 is referred to the Yellow-footed Antechinus. It is identified based on its small size (relative to other dasyurids), possessing a crowded premolar row, and a heavily reduced P₃ that retains two roots. The specimen is whitish in colour and was found on the surface suggesting that it is modern. Yellow-footed Antechinuses are common in eastern Australia.

• Sarcophilus harrisii

Fossils of marsupial devils were found in several of the caves (Table 1), although there are two clear size morphs present. The smaller-bodied species, Sarcophilus harrisii (Tasmanian Devil), is represented by a left mandible that is missing its teeth (AODF0915; Fig. 4B). Its identification is based on its large size (relative to other dasyurids), being robust (as opposed to slender as in Thylacinus), and possessing a low condyle in approximately the same plane as the tooth row. Although found on the surface of a deposit in Fig Tree Cave, the specimen is mineralised and a calcite crust had formed on the bone (although now removed following preparation), suggesting some antiquity. S. harrisii suffered extinction on the Australian mainland around 3,000–4,000 years ago (White et al., 2018). Thus, that timeframe indicates a minimum age for this specimen.

• Sarcophilus laniarius

A very large fossil devil is represented by several specimens including an isolated lower canine (AODF0916), a partial left maxilla with P³–M^1–3 (AODF0917; Fig. 4C), as well as broken and isolated molar teeth. The dentition is similar in gross morphology to modern Sarcophilus, but is extremely large in comparison (Table 2). The canine was found on the surface in Death Trap Cave, while the maxilla was recovered from a shallow, clay-rich deposit (that also included specimens of other megafaunal taxa) in Red-naped Cave. The youngest reliable date of S. laniarius on the continent is ca. 50 ka (Price et al., 2009b) while the oldest is ca. 500 ka (Prideaux et al., 2007). Thus, the Glenrock specimens are likely middle-late Pleistocene in age.

Peramelidae

• Isoodon obesulus

The Southern Brown Bandicoot is represented by several specimens including mandibles (e.g., AODF0918; Fig. 4D) from adult individuals, most of which are missing teeth. They are identified as Isoodon obesulus on the basis of possessing a steeply inclined vertical ramus (ca. 115°) relative to the horizontal ramus. This feature clearly distinguishes them from other peramelids such as Perameles (long-nosed bandicoots). The specimens are intermediate in size between the large I. macrourus and smaller I. auratus. Three of the eight caves surveyed contained skeletal elements of the Southern Brown Bandicoot (Table 1). All specimens were found on the surface of cave floors or within exposed crevices. The bones are white and unmineralised, suggesting that they are modern.

Phascolarctidae

• Phascolarctos stirtoni

A fossil lower right mandible (AODF0920; Figs. 5A and 5B) with P₃–M_1–4 is referred to the megafaunal Stirton’s Koala, Phascolarctos stirtoni. In gross morphology, the specimen is similar to the extant Koala, Phascolarctos cinereus. However, teeth of AODF0920 are up to 30% larger than the average size of equivalent dentition in the extant species and several are outside the entire size range of modern specimens (Table 3). The teeth are also smaller than the extremely large Pleistocene Phascolarctos yorkensis (see Table 3 of Pledge, 1992), the largest-known koala. The specimen is heavily mineralised and was substantially encrusted in calcite prior to preparation (it remains cemented to a macropodid femur and could not be removed without damaging the specimen. It is important to note that the calcite is impure and not suitable for radiometric dating, such as the U–Th method, e.g., Price et al., 2013). The specimen is from Red-naped Cave, in the same clay-rich deposit as the giant devil, AODF0917. The youngest geological age of Phascolarctos stirtoni is ca. 50 ka (Price et al., 2009b) whilst the oldest records are ca. 500 ka (Price, 2008). This suggests that the deposit is mid-late Pleistocene, and thus in agreement with the age suggested by the presence of the giant devil.

Thylacoleonidae

• Thylacoleo carnifex

A small, fossilised tooth fragment (AODF0922; Figs. 5C–5D) is wedged-shaped and includes some vertically orientated, striated enamel on one side and exposed dentine on the other. The specimen is from a relatively large-bodied organism, but is not referable to the Diprotodontoidea (giant wombat-like marsupials) as the enamel is too thin (ca. 0.8 mm) relative to the size of the fragment. Macropodoidea and Vombatidae are excluded as the tooth fragment is too broad and flat to be part of either a kangaroo’s or wombat’s dentition, respectively. Only marsupial ‘lions’ possess such striations in dental enamel, especially on the upper and lower thirds premolars (e.g., SAMP24101, Fig. 5E). A mastication-related, obliquely angled wear surface on the tooth fragment is typical of the lingual side of upper and lower P3s in Thylacoleo carnifex. Given that the wear surface is indicative of the occlusal face of the tooth, the height of the crown is similar to that in Thylacoleo carnifex. Thus, we consider the specimen is a fragment of a third premolar of Thylacoleo carnifex. Thylacoleo carnifex is the largest-bodied species within Thylacoleonidae, weighing up to 160 kg (Wroe et al., 1999). Of note, the specimen is from the same deposit in Red-naped Cave that produced other megafaunal taxa. The youngest fossil record of Thylacoleo carnifex is ca. 48 ka (Prideaux et al., 2010), while the oldest is ca. 500 ka (Prideaux et al., 2007), thus, is in agreement with a probable age of mid-late Pleistocene for the deposit.

Vombatidae

• Vombatus sp. indet.

Numerous fragmented and isolated teeth, as well as a partial lower left mandible (AODF0921; Fig. 5F) were found in three of the region’s caves. The species is a medium-sized wombat, within the size range of the extant Vombatus ursinus. Species of Vombatus differ from those of the other extant genus of wombat, Lasiorhinus, by having a mandible with its greatest depth below M₄, rather than M₃ (Dawson, 1983). The Glenrock mandible cannot be compared with the Pleistocene Vombatus hackettii as corresponding mandibular elements have not been reported (Dawson, 1983). The mandible is heavily mineralised, suggesting considerable antiquity. Vombatus ursinus occurs in the region today.

Phalangeridae

• Trichosurus sp. indet.

Brush-tailed possums are represented by isolated specimens from Fig Tree Cave and Death Trap caves including a left mandible (AODF0923; Fig. 6A). The short blade-like premolar is inflected outwards from the direction of the molar row. The molars are bilophodont. In terms of molar morphology, species of Trichosurus are somewhat similar to the rufus rat-kangaroo (Aepyprymnus rufescens), but isolated specimens from Glenrock lack a masseteric canal, a characteristic feature of kangaroos and their allies. AODF0923 is heavily mineralised, suggesting considerable antiquity, although brush-tailed possums continue to frequent the area today. This suggests that brush-tailed possums have occurred in the region for considerable time.

Macropodoidea

• Bettongia gaimardi

Several mandibles are referred to the Eastern Bettong (e.g., AODF0924 and AODF0925; Figs. 6B and 6C, respectively). They are characterised by possessing a long, blade-like P₃ that is angled anterobuccally relative to the molar row. The P₃ has seven vertical ridgelets on the buccal side and eight on the lingual side. The molars are bunodont (but tending towards bilophodonty), with a masseteric canal in the jaw. The angular process at the posterior of the jaw is long and pointed, more so than in species of Aepyprymnus. The bones were found as surface specimens on shallow sandy deposits of two caves (Table 1) and are largely unmineralised suggesting that they are modern. Natural populations of the Eastern Bettong are extinct on the mainland, but it survives in Tasmania.

• Notamacropus rufogriseus

The Red-necked Wallaby is represented by modern specimens within Red-naped Cave (e.g., AODF0926; Fig. 6D). They were identified on the basis of the medium-sized skull (relative to other macropodines) that has two large palatine-maxillary vacuities. The length of the P³ is less than that of the M². Specimens were found only in caves, but on the surface of subterranean deposits. The bones are unmineralised, slightly discoloured, and are likely modern. Red-necked Wallabies are extant in the region.

• Macropus giganteus giganteus

The modern Grey Kangaroo was recorded in several caves (Table 1), with additional fresh carcasses occasionally observed in various states of decay outside of the caves. They are characterised by a relatively large skull, small palatine vacuities, and variable fenestration on the palate (e.g., AODF0927; Fig. 6E). Subterranean specimens were occasionally observed, with some skeletons in near-complete articulation, suggesting minimal disturbance. The bones are generally white-ish in colour and unmineralised, indicating that such specimens are modern. Grey Kangaroos are extant in the region.

• Macropus giganteus titan

The Giant Grey Kangaroo is represented by a partial maxilla that contains two teeth (AODF0928; Fig. 6F). Although the specimen lacks specific diagnostic features (i.e., premolars; Bartholomai, 1975), it is most similar in size to specimens previously attributed to Macropus giganteus titan rather than other extinct, but smaller-sized species within the genus. The specimen is mineralised and was recovered from the megafaunal deposit within Red-naped Cave. Macropus giganteus titan is the largest species recorded in the region, with individuals estimated to weigh up to 180 kg (Helgen et al., 2006).

• Petrogale penicillata

Skeletal remains of Brush-tailed Rock Wallabies were recorded in several of the caves (Table 1). Identification of species of Petrogale is notoriously difficult considering the morphological similarities that exist between species (modern species are distinguished mostly on the basis of hair and soft tissue characters). However, given that the specimens are morphologically identical to Petrogale penicllata, and that it is the only known rock wallaby in the area, we consider the skeletal and dental remains referable to this species. Many of the bones are discoloured, but unmineralised suggesting that they are recent, although a fossil maxillary fragment (e.g., AODF0930; Fig. 6G) is recorded from the megafaunal deposit within Red-naped Cave. This record demonstrates that Brush-tailed Rock Wallabies have long frequented the Manning Karst Region.

• Wallabia bicolor

A single Swamp Wallaby skull was observed on the surface of Red-naped Cave (AODF0931; Fig. 6H). The skull is medium-sized (relative to other macropodines) with two large palatine-maxillary vacuities. The P³ is the longer than any individual molar. Similar to the Red-necked Wallaby, the bones are discoloured but unmineralised, and likely modern. Extant populations are common in eastern Australia.

Microchiroptera

• Microchiroptera gen. et sp. indet.

Post-cranial bones from bats were recorded as surface specimens in Westgate Cave (e.g., AODF0932; Fig. 7A). They lack features that allow diagnosis to the genus or species level. They are here referred to an indeterminate, but small-sized microchiropteran on the basis of their gracility in comparison to larger-bodied members of the suborder, such as megadermatids. They are also smaller than regionally extant fruit bats (megachiropterans). The bones are typically white in colour and unmineralisted, indicating their recent input into the cave deposits.

Muridae

• Conilurus albipes

The White-footed Rabbit Rat is represented by a maxilla and mandible fragment (AODF0933 and AODF0938; Figs. 7B and 7C, respectively) found in Fig Tree Cave. This is the largest species of murid at Glenrock. It was identified on the basis of possessing high-crowned molars with distinct cusps (rather than transverse lophs common in other murids). Cusp T7 is well-developed on the M¹ and M². The bones are white in colour and unmineralised, suggesting that they are modern. The species is extinct having not been recorded alive since the 1860s.

• Pseudomys gracilicaudatus

The Eastern Chestnut Mouse is represented by several maxillae (e.g., AODF0934; Fig. 7D) in Westgate Cave. In comparison to other species within the genus, Pseudomys gracilicaudatus is medium-sized and possesses relatively broad but low-crowned molars, anterior palatal foramena that extend past the anterior margin of the M¹, and (commonly) an accessory cusp on M¹. Specimens are unmineralised and collected from sandy surface deposits within the caves, suggesting that they are modern. Extant populations of the species have not been recorded in the Glenrock area.

• Pseudomys oralis

The Hastings River Mouse is represented by maxillae (e.g., AODF0935; Fig. 7E) found on surface deposits in several caves in the region (Table 1). The species is relatively large in comparison to other members of the genus. It possesses high crowned cusps, with significant reduction of the T1 cusp on the M¹. The anterior edge of the zygomatic plate is relatively straight. On the basis of preservation and occurrence within the caves, we suggest that the skeletal material of this species is modern. The Hastings River Mouse is found in forests in eastern New South Wales and south-east Queensland, but uncommonly encountered.

• Rattus sp. indet. (R. tunneyi or R. fuscipes)

Species of Rattus are represented by partial skulls and mandibles from several of the region’s caves (Table 1). They are identified by their size (medium-sized in comparison to other Australian murids), possessing additional roots on most molars (including five on M¹), sub-equal sized buccal and lingual cusps on M¹, as well as a supplementary cusp on the antero-buccal corner of M₂. Specimens from the Manning Karst Region (e.g., AODF0936; Fig. 7F) compare well with R. tunneyi (Pale Field Rat) and R. fuscipes (Bush Rat) in terms of molar dimensions and by possessing long anterior palatal foramena. These two species are difficult to separate purely on the basis of morphology. The specimens are unmineralised and were collected from the surface of deposits within the caves, suggesting that they are modern.

• Muridae gen. et sp. indet.

One partial skull (AODF0937; Fig. 7G) could not be assigned to any known species of Australian rodent, either native or introduced. It is distinguished by a combination of the following features: medium-sized (similar in size to Rattus spp.) with a strongly constricted interorbital region, zygomatic plate that has a slightly concave anterior margin, broad anterior palatal foramena that are rounded posteriorly and end anterior of M¹, deep furrows in the hard palate that connect the anterior palatal foramina to the posterior palatal foramina, and two lingual roots on M¹. The constricted interorbital region is otherwise only seen in Pseudomys auritus (a very poorly known species), but the other features mentioned above are significantly different. The molars are worn, but the arrangement of cusps appear to resemble those of Pseudomys australis. It is possible that this specimen represents an undescribed species, but we reserve judgement on its taxonomy until more material comes to hand. The specimen was collected from the surface of Westgate Cave and is unmineralised, suggesting that it is modern.

Canidae

• Vulpes vulpes

A skull of the Red Fox was observed as a surface specimen in Red-naped cave. The specimen is discoloured and unmineralised, indicating that it is modern. Foxes were introduced into Australia during the 19th century.

• Canis familiaris

Numerous dog skeletons were observed on the surface of Ewe Beaut Cave. We attribute these specimens to wild dogs introduced by Europeans rather than the ‘purebred’ Dingo (both taxa are Canis familiaris, following Jackson et al., 2017) on the basis of them being slightly more brachiocephalic than the latter. The specimens are discoloured but unmineralised and clearly modern. A discarded margarine container was found partially buried adjacent to the dog skeletons. The use-by date printed on the bottom is July 1982, thus providing an approximate age of the skeletons.

Bovidae

• Ovis aries

Sheep skeletons were observed in several of the caves, including Ewe Beaut Cave. Similar to other specimens from this cave floor (as others in the area), the skeletons are slightly discoloured and modern. Sheep were introduced to Australia in 1797.

Leporidae

• Oryctolagus cuniculus

Skeletal material of Rabbits were observed as surface specimens on the floor of Lonesome Lair Cave. Rabbits are easily distinguished from Hares (Lepus europaeus) by possessing a more gently inclined vertical ramus relative to the horizontal ramus of the mandible. The bones are unmineralised and modern. Rabbits were introduced to the continent in the 18th century, but feral populations are thought to have become established in the mid-19th century.