Chromosome-level genome provides insight into the evolution and conservation of the threatened goral (Naemorhedus goral)

BACKGROUND

Gorals Naemorhedus resemble both goats and antelopes, which prompts much debate about the intragenus species delimitation and phylogenetic status of the genus Naemorhedus within the subfamily Caprinae. Their evolution is believed to be linked to the uplift of the Qinghai-Tibet Plateau (QTP). To better understand its phylogenetics, the genetic information is worth being resolved.

RESULTS

Based on a sample from the eastern margin of QTP, we constructed the first reference genome for Himalayan goral Naemorhedus goral, using PacBio long-read sequencing and Hi-C technology. The 2.59 Gb assembled genome had a contig N50 of 3.70 Mb and scaffold N50 of 106.66 Mb, which anchored onto 28 pseudo chromosomes. A total of 20,145 protein-coding genes were predicted in the assembled genome, of which 99.93% were functionally annotated. Phylogenetically, the goral was closely related to muskox on the mitochondrial genome level and nested into the takin-muskox clade on the genome tree, rather than other so-called goat-antelopes. The cladogenetic event among muskox, takin and goral occurred sequentially during the late Miocene (~ 11 - 5 Mya), when the QTP experienced a third dramatic uplift with consequent profound changes in climate and environment. Several chromosome fusions and translocations were observed between goral and takin/muskox. The expanded gene families in the goral genome were mainly related to the metabolism of drugs and diseases, so as the positive selected genes. The Ne of goral continued to decrease since ~ 1 Mya during the Pleistocene with active glaciations.

CONCLUSION

The high-quality goral genome provides insights into the evolution and valuable information for the conservation of this threatened group.

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.

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.