Complete mitochondrial genome of the Himalayan serow (Capricornis thar) and its phylogenetic status within the genus Capricornis

Chromosome-Level Genome Assembly for the Chinese Serow (Capricornis milneedwardsii) Provides Insights Into Its Taxonomic Status and Evolution

Chinese serow (Capricornis milneedwardsii) is mainly distributed in the south of Yellow River in China, which has been listed as vulnerable by the International Union for Conservation of Nature (IUCN). However, the reference genome of serow has not been reported and its taxonomic status is still unclear. Here, we first constructed a high-quality chromosome-level reference genome of C. milneedwardsii using PacBio long HiFi reads combined with Hi-C technology. The assembled genome was ~2.83 Gb in size, with a contig N50 of 100.96 Mb and scaffold N50 of 112.75 Mb, which were anchored onto 24 chromosomes. Furthermore, we found that the Chinese serow was more closely related to muskox, which diverged from ~4.85 million years ago (Mya). Compared to the karyotype of goat (2n = 60), we found the Chinese serow (2n = 48) experienced six chromosome fusions, which resulted in the formation of six central centromere chromosomes. We also identified two positively selected genes (MYH6 and DCSTAMP) specific to Chinese serow, which were involved in 'viral myocarditis' and 'Cardiac muscle contraction'. Interestingly, compared to other Caprinae animals, the MYH6 protein of Chinese serow occurred two mutations (E1520S and G1521S), which might be related to hypoxia tolerance. The high-quality reference genome of C. milneedwardsii provides a valuable information for protection of serows and insights into its evolution.

Ancient Mitogenomes Reveal Stable Genetic Continuity of the Holocene Serows

As one of the remaining species of Caprinae only found in Asia, serows (Capricornis) and their classification and conservation have received increasing attention in recent years. However, their evolutionary history and population dynamics are not yet clear. To shed light on these topics, we report the first near-complete ancient mitochondrial genomes from two serow sub-fossils (CADG839 and CADG946) dating to 8860 ± 30 years and 2450 ± 30 years, and incorporate the newly obtained mitogenomes into the dataset of living serows (18 complete mitochondrial genomes drawn from National Center for Biotechnology Information, NCBI) to investigate their relationships and evolution. Phylogenetic results support four clades of serows that can be further divided into five subclades, indicating higher genetic diversity than previously thought. Notably, our two ancient samples do not form a separate branch but belong to Capricornis sumatraensis clade A together with modern individuals, which suggests genetic continuity between ancient and modern serows. Furthermore, our results suggest that the maternal divergences of serows occurred at the beginning of the Pleistocene. Bayesian estimation indicates that the first divergence among all serows happened approximately 2.37 Ma (95% highest posterior density, HPD: 2.74-2.02 Ma) when Japanese serow (Capricornis crispus) appeared, while the last divergence occurred within the Sumatran serow (C. sumatraensis clade A and B) around 0.37-0.25 Ma. Additionally, we found the effective maternal population size of C. sumatraensis increased around 225-160 and 90-50 ka, then remained stable since 50 ka. Overall, our study provides new insights into serow phylogeny and evolutionary history.

Complete mitochondrial genome of Manispentadactylapentadactyla (Mammalia: Pholidota), an endemic subspecies of Chinese pangolin: mitogenome characterisation and phylogenetic implications

The Chinese pangolin Manispentadactyla is critically endangered because of over-exploitation and illegal trafficking and includes three subspecies. However, the taxonomic status of the three subspecies of the Chinese pangolin has not been well resolved, which impedes regional conservation and illegal trade traces. In this study, the complete mitogenome sequence of M.p.pentadactyla, an endemic subspecies of the Chinese pangolin in Taiwan, was determined. The complete mitogenome of M.p.pentadactyla is 16,570 base pairs (bp) in length with 13 protein-coding genes (PCG), 23 transfer RNAs (tRNAs), two ribosomal RNAs and a 1164 bp control region. The overall base composition of the genome showed a slight A + T bias (59.9%), positive AT skew (0.1515) and negative GC skew (-0.3406), which is similar to that of other pangolins. All PCGs started with a typical ATN codon and all tRNAs were typical cloverleaf-shaped secondary structures, except for tRNA-Ser^(GCU). Phylogenetic analysis indicated a monophyletic relationship for M.p.pentadactyla and M.p.aurita and was monophyletic for M.p.pentadactyla, but paraphyletic for M.p.aurita. The paraphyly of M.p.aurita resulted from an incomplete lineage sorting. This study enriched the mitogenome database of the Chinese pangolin and the molecular information obtained should be very useful for future research on mitogenome evolution and genetic diversification in M.pentadactyla.

Activity Rhythms of Coexisting Red Serow and Chinese Serow at Mt. Gaoligong as Identified by Camera Traps

Simple Summary

How congeneric species with similar realized niches manage to coexist is a central question in the study of biodiversity. Here, we examined the daily activity rhythm of two coexisting serow species in a mid-mountain humid evergreen broadleaf forest. We used camera traps in a five-year survey at Mt. Gaoligong, western Yunnan, China. We compared the daily activity rhythm of the rare red serow (Capricornis rubidus), a medium-sized solitary ungulate, with the coexisting Chinese serow (C. milneedwardsii milneedwardsii). Although their overall daily activity rhythms were similar, the rare red serow tended to range, feed, and stay vigilant from afternoon through midnight throughout the year. By contrast, Chinese serows preferred to be active from sunrise to noon in the wet season, but shifted their activities and behaviors to afternoon and midnight in the dry season. Interestingly, we found red serows sometimes ranging together with Chinese serows. When they encountered each other, red serows altered their activity patterns more notably, while Chinese serows significantly increased their activity level. These findings are understandable given their similar resource requirements. Although exploitative competitors, red and Chinese serow coexist by avoiding interference competition by altering their respective activity patterns in time.

Abstract

Surveying the activity rhythms of sympatric herbivorous mammals is essential for understanding their niche ecology, especially for how they partition resources and their mechanisms of coexistence. Over a five-year period, we conducted infrared camera-trapping to monitor the activity rhythms of coexisting red serow (Capricornis rubidus) and Chinese serow (C. milneedwardsii milneedwardsii) in the remote mountainous region of Pianma, Mt. Gaoligong, Yunnan, China. Cameras captured images of red serow and Chinese serow on 157 and 179 occasions, respectively. We used circular kernel density models to analyze daily activity rhythms and how temporal variations in activity ensure their co-existence. Although their overall activity levels and patterns were similar, temporal activity and behavior partitioning among the two species occurred during the wet season. Compared with Chinese serows, red serows exhibited less variable daily activity levels, patterns, as well as feeding and vigilance behaviors between seasons. When the two species occasionally ranged together, red serows tended to alter their activity pattern while Chinese serows significantly increased their activity level. Red serow and Chinese serow are exploitative competitors but coexist by altering their daily activity rhythms when in contact and changing activity patterns during the wet season, enabling their coexistence.

Mitochondrial genomes of African pangolins and insights into evolutionary patterns and phylogeny of the family Manidae

BACKGROUND

This study used next generation sequencing to generate the mitogenomes of four African pangolin species; Temminck's ground pangolin (Smutsia temminckii), giant ground pangolin (S. gigantea), white-bellied pangolin (Phataginus tricuspis) and black-bellied pangolin (P. tetradactyla).

RESULTS

The results indicate that the mitogenomes of the African pangolins are 16,558 bp for S. temminckii, 16,540 bp for S. gigantea, 16,649 bp for P. tetradactyla and 16,565 bp for P. tricuspis. Phylogenetic comparisons of the African pangolins indicated two lineages with high posterior probabilities providing evidence to support the classification of two genera; Smutsia and Phataginus. The total GC content between African pangolins was observed to be similar between species (36.5% - 37.3%). The most frequent codon was found to be A or C at the 3rd codon position. Significant variations in GC-content and codon usage were observed for several regions between African and Asian pangolin species which may be attributed to mutation pressure and/or natural selection. Lastly, a total of two insertions of 80 bp and 28 bp in size respectively was observed in the control region of the black-bellied pangolin which were absent in the other African pangolin species.

CONCLUSIONS

The current study presents reference mitogenomes of all four African pangolin species and thus expands on the current set of reference genomes available for six of the eight extant pangolin species globally and represents the first phylogenetic analysis with six pangolin species using full mitochondrial genomes. Knowledge of full mitochondrial DNA genomes will assist in providing a better understanding on the evolution of pangolins which will be essential for conservation genetic studies.