The Middle Pleistocene vertebrate fauna from Khok Sung (Nakhon Ratchasima, Thailand): biochronological and paleobiogeographical implications

The Holocene record of the slow loris (Nycticebus sp.) in Java (Indonesia)

OBJECTIVES

(Sub)fossil lorises are rare in Southeast Asia. Their taxonomic relationship with extant populations, and the extent to which their distribution and morphology are influenced by changing environmental conditions, remains poorly understood. This study provides a synthesis of Nycticebus occurrences in Holocene Java. A morphometric analysis of a sample of craniodental remains aims to improve our understanding of their taxonomic status. Morphometrics were also used to explore potential size changes during the Holocene.

MATERIALS AND METHODS

Based on the literature and a review of museum catalogs, a synthesis was compiled of (sub)fossil slow loris occurrences in Java. Morphometric data on the mandible and maxilla of 10 (sub)fossil lorises were compared with a dataset of extant specimens to assess variation in size and shape.

RESULTS

Five Holocene Nycticebus occurrences were identified in eastern Java. All specimens fall in the range of N. javanicus and N. coucang. The specimens from Hoekgrot, Gua Jimbe, and Sampung suggest an affinity to N. javanicus. The remains from Gua Jimbe and Hoekgrot gave values close to the largest N. javanicus specimens, but the (presumably older) Song Terus specimen was of average size.

DISCUSSION AND CONCLUSIONS

The distribution of Nycticebus suggests that it originally occurred throughout the island. The remains are probably best identified as N. javanicus or N. coucang, but the Neolithic finds from Hoekgrot and Gua Jimbe are presumably N. javanicus. Size variation in Nycticebus was clinal, but although some large specimens were present, no evidence was found for size diminution during the Holocene.

Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina)

Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.

An extinct deep-snouted Alligator species from the Quaternary of Thailand and comments on the evolution of crushing dentition in alligatorids

Fossil Alligator remains from Asia are critical for tracing the enigmatic evolutionary origin of the Chinese alligator, Alligator sinensis, the only living representative of Alligatoridae outside the New World. The Asian fossil record is extremely scarce and it remains unknown whether A. sinensis is an anagenetic lineage or alternatively, extinct divergent species were once present. We provide a detailed comparative description of a morphologically highly distinct Alligator skull from the Quaternary of Thailand. Several autapomorphic characters warrant the designation of a new species. Alligator munensis sp. nov. shares obvious derived features with A. sinensis but autapomorphies imply a cladogenetic split, possibly driven by the uplift of the southeastern Tibetan plateau. The presence of enlarged posterior alveoli in Alligator munensis is most consistent with a reversal to the alligatorine ancestral condition of having crushing dentition, a morphology strikingly absent among living alligatorids. Crushing dentition has been previously considered to indicate an ecological specialisation in early alligatorines that was subsequently lost in Alligator spp. However, we argue that there is yet no evidence for crushing dentition reflecting an adaptation for a narrower niche, while opportunistic feeding, including seasonal utilisation of hard-shelled preys, is a reasonable alternative interpretation of its function.

Dental mesowear and microwear for the dietary reconstruction of Quaternary Southeast Asian serows and gorals

Serows and gorals (Bovidae, Caprinae) are emblematic antelopes distributed in Southeast Asia. They all are nearly threaten or vulnerable species nowadays despite having a more widespread distribution during the Pleistocene. Fossils of three native caprine species, i.e., a Sumatran serow Capricornis sumatraensis, Chinese goral Naemorhedus griseus, and Himalayan goral Naemorhedus goral, were recovered from four Pleistocene paleontological and archeological sites in Thailand, namely Pha Bong, Khok Sung, Tham Wiman Nakin, and Tham Lod Rockshelter. To investigate dietary changes of these Southeast Asian serows and gorals through the Quaternary, differences in feeding habits and habitat preferences between the Pleistocene and extant populations were examined using the hypsodonty index (HI) together with the mesowear II method and the dental microwear texture analysis (DMTA). The HI and mesowear-II results showed that Pleistocene and extant caprines were mixed feeders. For the Pleistocene caprine populations, the DMTA results suggested more browsing signals for C. sumatraensis than both Naemorhedus species that were mixed feeders similar to their extant populations. The DMTA demonstrated a considerable dietary overlap among the Pleistocene sympatric caprine populations. The dental microwear results also revealed that the extant C. sumatraensis is a leaf-dominant browser, while the extant N. griseus possibly feeds on seeds or tough food items. These data combined with previous stable carbon isotope analyses reinforce the idea that the restricted ranges of habitats for these extant serow and goral populations have possibly been driven by the Holocene climatic and environmental changes as well as the negative effects of human activities.

Gigantopithecus blacki (Primates, Ponginae) from the Lang Trang Cave (Northern Vietnam): The Latest Gigantopithecus in the Late Pleistocene?

The dental remains of Gigantopithecus blacki von Koenigswald, 1935 (a complete right m2 with roots and distal fragment of left m2 crown) from the Upper Pleistocene deposits of the Lang Trang cave in northern Vietnam (Thanh Hoa Province) are described. It is the first record of Gigantopithecus in the Upper Pleistocene of Vietnam and, apparently, the second one in the Upper Pleistocene in general (considering material from Shuangtan cave in southern China). Probably, the extinction of G. blacki was confined to the Middle-Late Pleistocene transition, and the specimens from the Lang Trang cave belong to one of the latest relict populations of Gigantopithecus.

A Middle Pleistocene Denisovan molar from the Annamite Chain of northern Laos

The Pleistocene presence of the genus Homo in continental Southeast Asia is primarily evidenced by a sparse stone tool record and rare human remains. Here we report a Middle Pleistocene hominin specimen from Laos, with the discovery of a molar from the Tam Ngu Hao 2 (Cobra Cave) limestone cave in the Annamite Mountains. The age of the fossil-bearing breccia ranges between 164–131 kyr, based on the Bayesian modelling of luminescence dating of the sedimentary matrix from which it was recovered, U-series dating of an overlying flowstone, and U-series–ESR dating of associated faunal teeth. Analyses of the internal structure of the molar in tandem with palaeoproteomic analyses of the enamel indicate that the tooth derives from a young, likely female, Homo individual. The close morphological affinities with the Xiahe specimen from China indicate that they belong to the same taxon and that Tam Ngu Hao 2 most likely represents a Denisovan.

Evidence for the presence of Homo during the Middle Pleistocene is limited in continental Southeast Asia. Here, the authors report a hominin molar from Tam Ngu Hao 2 (Cobra Cave), dated to 164–131 kyr. They use morphological and paleoproteomic analysis to show that it likely belonged to a female Denisovan.

A new rhinoceros clade from the Pleistocene of Asia sheds light on mammal dispersals to the Philippines

Rhinoceroses are among the most endangered mammalian species today. Their past diversity is well documented from the Eocene onward, although their evolutionary history is far from being fully understood. Here, we elucidate the systematic affinities of a Pleistocene rhinoceros species represented by a partial skeleton from 709 ± 68 kya archaeological deposits in Luzon Island, Philippines. We perform a comprehensive phylogenetic analysis, including all living species and a wide array of extinct rhinocerotid species. We confirm the early split between Elasmotheriinae and Rhinocerotinae at c. 35.5 Mya and constrain the divergence between recent Asian and African rhinoceroses at c. 24 Mya, with contrasting phenotypic evolutionary rates in Diceroti and Rhinoceroti. Dental features reveal the existence of an unsuspected Asian Pleistocene clade, referred to as Nesorhinus gen. nov.. It includes the rhinoceros from the Philippines and another extinct species from Taiwan, N. hayasakai. Nesorhinus is the sister-group to a cluster comprising Dicerorhinus and Rhinoceros. Our phylogenetic results strongly suggest an island-hopping dispersal for Nesorhinus, from the Asian mainland towards Luzon via Taiwan by the Late Miocene or later, and Pleistocene dispersals for representatives of Rhinoceros. Nesorhinus philippinensis would be the first perissodactyl species supporting the island-rule hypothesis, with decreased body weight and limb-bone robustness.

Population genetics and evolutionary history of the endangered Eld's deer (Rucervus eldii) with implications for planning species recovery

Eld's deer (Rucervus eldii) with three recognised subspecies (R. e. eldii, R. e. thamin, and R. e. siamensis) represents one of the most threatened cervids found in Southeast Asia. The species has experienced considerable range contractions and local extinctions owing to habitat loss and fragmentation, hunting, and illegal trade across its distribution range over the last century. Understanding the patterns of genetic variation is crucial for planning effective conservation strategies. This study investigated the phylogeography, divergence events and systematics of Eld's deer subspecies using the largest mtDNA dataset compiled to date. We also analysed the genetic structure and demographic history of R. e. eldii using 19 microsatellite markers. Our results showed that R. e. siamensis exhibits two divergent mtDNA lineages (mainland and Hainan Island), which diverged around 0.2 Mya (95% HPD 0.1-0.2), possibly driven by the fluctuating sea levels of the Early Holocene period. The divergence between R. e. eldii and R. e. siamensis occurred around 0.4 Mya (95% HPD 0.3-0.5), potentially associated with the adaptations to warm and humid climate with open grassland vegetation that predominated the region. Furthermore, R. e. eldii exhibits low levels of genetic diversity and small contemporary effective population size (median = 7, 4.7-10.8 at 95% CI) with widespread historical genetic bottlenecks which accentuates its vulnerability to inbreeding and extinction. Based on the observed significant evolutionary and systematic distance between Eld's deer and other species of the genus Rucervus, we propose to classify Eld's deer (Cervus eldii) in the genus Cervus, which is in congruent with previous phylogenetic studies. This study provides important conservation implications required to direct the ongoing population recovery programs and planning future conservation strategies.

Ancient DNA from the Asiatic Wild Dog (Cuon alpinus) from Europe

The Asiatic wild dog (Cuon alpinus), restricted today largely to South and Southeast Asia, was widespread throughout Eurasia and even reached North America during the Pleistocene. Like many other species, it suffered from a huge range loss towards the end of the Pleistocene and went extinct in most of its former distribution. The fossil record of the dhole is scattered and the identification of fossils can be complicated by an overlap in size and a high morphological similarity between dholes and other canid species. We generated almost complete mitochondrial genomes for six putative dhole fossils from Europe. By using three lines of evidence, i.e., the number of reads mapping to various canid mitochondrial genomes, the evaluation and quantification of the mapping evenness along the reference genomes and phylogenetic analysis, we were able to identify two out of six samples as dhole, whereas four samples represent wolf fossils. This highlights the contribution genetic data can make when trying to identify the species affiliation of fossil specimens. The ancient dhole sequences are highly divergent when compared to modern dhole sequences, but the scarcity of dhole data for comparison impedes a more extensive analysis.

Pleistocene Mammals from the Lang Trang Cave (Vietnam): New Data

The following mammal assemblage was identified among the materials collected in 2020 from the Pleistocene of the Lang Trang cave (northern Vietnam): the primates Pongo sp., Trachypithecus sp., Macaca cf. nemestrina (Linnaeus, 1766), and Macaca sp.; the carnivorans Arctonyx collaris rostratus Matthew et Granger, 1923 and Panthera sp.; the chiropteran Ia io Thomas, 1902; the rodent Hystrix kiangsenensis Wang, 1931; the proboscidean Elephas sp.; the perissodactyls Tapirus indicus (Desmarest, 1819) and Dicerorhinus sumatrensis (Fischer, 1814); the artiodactyls Sus scrofa Linnaeus, 1758, S. barbatus Müller, 1838, Tragulus kanchil (Raffles, 1821), Hydropotes inermis Swinhoe, 1870, Muntiacus muntjak (Zimmermann, 1780), Axis porcinus (Zimmermann, 1780), Rusa unicolor (Kerr, 1792), and Capricornis sumatraensis (Bechstein, 1799). I. io, S. barbatus, T. kanchil, H. inermis, and A. porcinus were detected in the Lang Trang fauna for the first time. The mammal assemblage is dominated by inhabitants of tropical forests (from lowlands to mountains), subtropical forms are also present.

Great Evening Bat Ia io (Vespertilionidae, Chiroptera) from the Pleistocene of Vietnam (Lang Trang Cave)

A dentary fragment of a great evening bat Ia io Thomas, 1902 found in 2020 in the Pleistocene deposits of the Lang Trang karstic cave in northern Vietnam is described. This rare species of large tropical bats now inhabits Nepal, eastern India, southern China, Thailand, Laos, and Vietnam and as a fossil is known from the Pleistocene of China. In Vietnam the fossil remains of this species have been discovered for the first time. By the total size and lower molar structure, the specimen from the Lang Trang cave is most similar to the subspecies Ia io peninsulata Soisook et al., 2017 that now occurs in southern Thailand.

Greater Hog Badger Arctonyx collaris (Mustelidae, Carnivora) from the Pleistocene of Vietnam (Lang Trang Cave)

The dental remains of a large badger collected in 2020 from the Pleistocene deposits of the Lang Trang karstic cave in northern Vietnam are described. The molars М¹ and М₁ exhibit the features that are characteristic of Arctonyx collaris Cuvier, 1825. At the same time, the length of M₁ of the Lang Trang form exceeds that of modern greater hog badgers. Based on the size and structure of the teeth, it can be assigned to the subspecies A. c. rostratus Matthew et Granger, 1923 known from the Pleistocene of China and Southeast Asia.

Oldest co-occurrence of Varanus and Python from Africa-first record of squamates from the early Miocene of Moghra Formation, Western Desert, Egypt

Lizard and snake remains from the early Miocene (Burdigalian) of the Moghra Formation, Egypt, are described herein. This material comprises the first fossil remains of squamates recovered from the otherwise rich and well known vertebrate assemblage of Moghra. The material pertains to two different genera, the varanid lizard Varanus and the pythonid snake Python and adds to the so far rather poorly known squamate fossil record from Africa. On the basis of the new remains, Moghra marks the oldest so far described co-occurrence of Varanus and Python in the African continent. The close sympatry of these two genera in the African fossil record is thoroughly analyzed and discussed, a co-existence, which is still widespread in the extant herpetofauna of the continent. Situated rather close to the so called "Levantine Corridor" and dated at the Burdigalian, practically when Afro-Arabia collided with Eurasia, the Moghra squamate assemblage offers the potential of important insights in the biogeography and dispersal events of vertebrate groups during the early Miocene.

An 11 000-year-old giant muntjac subfossil from Northern Vietnam: implications for past and present populations

Described at the end of the twentieth century, the large-antlered or giant muntjac, Muntiacus gigas (syn. vuquangensis), is a Critically Endangered species currently restricted to the Annamite region in Southeast Asia. Here we report subfossil evidence of giant muntjac, a mandible fragment dated between 11.1 and 11.4 thousand years before present, from northern Vietnam. We describe morphological and metric criteria for diagnosis and consider the specimen in the context of regional archaeological and palaeontological records of Muntiacus. We then consider the palaeoenvironmental context of the specimen and the implications for habitat requirements for extant populations. The new specimen extends the known spatial and temporal range of giant muntjacs in Vietnam and is further evidence that this species was more widely distributed in the Holocene than current records indicate. While regional proxy evidence indicates a drier climate and more open woodland habitats at the onset of the Holocene, contextual evidence indicates that the specimen derived from an animal inhabiting limestone karst forest. This record also supports the assertion that remnant populations are in a refugial state, as a result of anthropogenic pressures, rather than representing a centre of endemism. These facts underscore the urgent need for the conservation of remaining populations.