2021 Vol. 42, No. 6
Diversifying on the Ark: multiple new endemic lineages of dwarf geckos from the Western Ghats provide insights into the systematics and biogeography of South Asian Cnemaspis (Reptilia: Squamata)
2021, 42(6): 675-691. doi: 10.24272/j.issn.2095-8137.2021.074
The highly speciose gekkonid genus Cnemaspis Strauch, 1887 is polyphyletic, with three distantly related and geographically isolated clades from Africa, South Asia (SA), and Southeast Asia. At present, there are 85 known species within SA Cnemaspis, although the number continues to increase rapidly with focused surveys and rigorous taxonomic work. Recent studies have provided valuable insights into the diversity and evolutionary history of SA Cnemaspis; however, most of these studies lack sufficient sampling in the Western Ghats (WG), where the genus has its greatest diversity. We addressed this research gap by conducting extensive sampling across the WG and re-examining museum specimens, thus providing a systematic account of various extant Cnemaspis species along with their distribution and natural history. We described 12 new species and a southern WG endemic clade of SA Cnemaspis. Ten of the newly described species are endemic to the forests of the southern WG. We also identified 10 well-supported subclades that can be separated across morphological, geographic, and phylogenetic axes. A time-calibrated phylogeny and ancestral area reconstructions confirmed the Paleocene origin of SA Cnemaspis in the WG and provide insights into its evolutionary history and biogeography. The discovery of multiple endemic and deeply divergent lineages further highlights the evolutionary significance of the WG for lizards.
The Chinese tree shrew (Tupaia belangeri chinensis) is emerging as an important experimental animal in multiple fields of biomedical research. Comprehensive reference genome annotation for both mRNA and long non-coding RNA (lncRNA) is crucial for developing animal models using this species. In the current study, we collected a total of 234 high-quality RNA sequencing (RNA-seq) datasets and two long-read isoform sequencing (ISO-seq) datasets and improved the annotation of our previously assembled high-quality chromosome-level tree shrew genome. We obtained a total of 3 514 newly annotated coding genes and 50 576 lncRNA genes. We also characterized the tissue-specific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome. We identified 144 tree shrew-specific gene families, including interleukin 6 (IL6) and STT3 oligosaccharyltransferase complex catalytic subunit B (STT3B), which underwent significant changes in size. Comparison of the overall expression patterns in tissues and pathways across four species (human, rhesus monkey, tree shrew, and mouse) indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level. Notably, the newly annotated purine rich element binding protein A (PURA) gene and the STT3B gene family showed dysregulation upon viral infection. The updated version of the tree shrew genome annotation (KIZ version 3: TS_3.0) is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models.
The Chantecler chicken, a unique Canadian indigenous breed, is well adapted to extremely cold environments. However, its genetic characteristics have not been well studied. Here, we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens, which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding. Based on a genome-wide scan, we identified two vital candidate regions containing ME3 and ZNF536, which are related to fat metabolism and nervous system in cold adaptation, respectively. We also found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions, such as northern China. Our study indicated that specialized commercial chickens in the early 20th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time. These findings enrich our understanding of the adaptive potential of commercial species.
SOX9 (SRY-related HMG box gene 9) is an essential regulator of male sex determination and testis differentiation in many vertebrate species. However, the functional role of Sox9 in testis differentiation has not yet been identified in any reptilian species. Herein, Sox9 knockdown in the red-eared slider turtle (Trachemys scripta) embryos at a male-producing temperature led to complete male-to-female sex reversal, characterized by the formation of an ovary-like structure, disappearance of male marker AMH, and ectopic expression of ovarian regulator FOXL2, as well as a female distribution pattern of germ cells. Conversely, in-ovo overexpression of Sox9 at a female-producing temperature resulted in partial masculinization of putative female embryos, with the co-existence of AMH and FOXL2. Our study provides the first direct evidence that Sox9 is indispensable for testicular differentiation in a reptilian species, further confirming the conserved role of Sox9 in vertebrate sexual development.
We report a new species of the genus Micryletta from the montane evergreen forest in the Bidoup-Nui Ba National Park, Lam Dong Province, Langbian Plateau, southern Vietnam, based on molecular and morphological evidence. The new species is diagnosed by a combination of the following morphological characters: body size small (snout-vent length (SVL) 22.4 mm, single female); iris uniform black; snout nearly truncate in dorsal view, slightly rounded in profile; tibiotarsal articulation of adpressed limb reaching level of eye; dorsal surface smooth; supratympanic fold present, prominent; outer metatarsal tubercle absent; tips of toes very weakly dilated into small discs; finger webbing absent, toe webbing rudimentary; dorsal surfaces of head and body orange-red with small irregularly shaped dark-brown patches; dorsal surface of limbs pale dark brown with small reddish speckles; body flanks dark brown anteriorly fading to grayish brown posteriorly with brown spots in groin area; lateral sides of head immaculate blackish brown without white patches; coloration of ventral surfaces immaculate dark gray. The new species is divergent from all other congeners in 16S rRNA gene sequences (2.6%–5.8%). Following the IUCN Red List Categories and Criteria, we propose the new species be listed as Data Deficient (DD).
The small-eared shrew genus Cryptotis is the third largest in the family Soricidae and occurs in North, Central, and northern South America. In Mexico and Central and South America, most species inhabit geographically isolated moist, montane habitats at middle and high elevations in a typical sky-island pattern. The 49 recognized species have been partitioned into as many as six species groups based on morphological and molecular phylogenetic studies. The relationships among these species groups are poorly resolved, and their evolutionary histories, including migration patterns and locomotor adaptations, remain unclear. Herein, we provide a new phylogeny incorporating complete mitochondrial genomes (mitogenomes) and supermatrix approach. We compared different evolutionary scenarios using approximately unbiased (AU), Kishino-Hasegawa (KH), and Shimodaira-Hasegawa (SH) statistical tests. The phylogenetic hypothesis based on mitogenomes revealed novel relationships supporting a basal position for the Cryptotis parvus-group in the genus, and a close relationship between C. gracilis and one clade of the C. thomasi-group. The former relationship is consistent with the least derived humerus morphology and northern distribution of the species. The latter relationship implies multiple migrations between Central and South America. The lack of fine resolution for the species group relationships may be due partly to the lack of taxon sampling. In contrast, multi-approach analyses suggest that the unresolved relationships may be a result of rapid diversification during the early stages of Cryptotis evolution.
Oxygen is an essential molecule for animal respiration, growth, and survival. Unlike in terrestrial environments, contamination and climate change have led to the frequent occurrence of hypoxia in aquatic environments, thus impacting aquatic animal survival. However, the adaptative mechanisms underlying fish responses to environmental hypoxia remain largely unknown. Here, we used large yellow croaker (Larimichthys crocea) and large yellow croaker fry (LYCF) cells to investigate the roles of the Hif-1α/Hsf1/Hsp70 signaling pathway in the regulation of cellular redox homeostasis, and apoptosis. We confirmed that hypoxia induced the expression of Hif-1α, Hsf1, and Hsp70 in vivo and in vitro. Genetic Hsp70 knockdown/overexpression indicated that Hsp70 was required for maintaining redox homeostasis and resisting oxidative stress in LYCF cells under hypoxic stress. Hsp70 inhibited caspase-dependent intrinsic apoptosis by maintaining normal mitochondrial membrane potential, enhancing Bcl-2 mRNA and protein expression, inhibiting Bax and caspase3 mRNA expression, and suppressing caspase-3 and caspase-9 activation. Hsp70 suppressed caspase-independent intrinsic apoptosis by inhibiting nuclear translocation of apoptosis-inducing factor (AIF) and disturbed extrinsic apoptosis by inactivating caspase-8. Genetic knockdown/overexpression of Hif-1α and dual-luciferase reporter assay indicated that Hif-1α activated the Hsf1 DNA promoter and enhanced Hsf1 mRNA transcription. Hsf1 enhanced Hsp70 mRNA transcription in a similar manner. In summary, the Hif-1α/Hsf1/Hsp70 signaling pathway plays an important role in regulating redox homeostasis and anti-apoptosis in L. crocea under hypoxic stress.
The pygmy marmoset, the smallest of the anthropoid primates, has a broad distribution in Western Amazonia. Recent studies using molecular and morphological data have identified two distinct species separated by the Napo and Solimões-Amazonas rivers. However, reconciling this new biological evidence with current taxonomy, i.e., two subspecies, Cebuella pygmaea pygmaea (Spix, 1823) and Cebuella pygmaea niveiventris (Lönnberg, 1940), was problematic given the uncertainty as to whether Spix’s pygmy marmoset (Cebuella pygmaea pygmaea) was collected north or south of the Napo and Solimões-Amazonas rivers, making it unclear to which of the two newly revealed species the name pygmaea would apply. Here, we present the first molecular data from Spix’s type specimen of Cebuella pygmaea, as well as novel mitochondrial genomes from modern pygmy marmosets sampled near the type locality (Tabatinga) on both sides of the river. With these data, we can confirm the correct names of the two species identified, i.e., C. pygmaea for animals north of the Napo and Solimões-Amazonas rivers and C. niveiventris for animals south of these two rivers. Phylogenetic analyses of the novel genetic data placed into the context of cytochrome b gene sequences from across the range of pygmy marmosets further led us to re-evaluate the geographical distribution for the two Cebuella species. We dated the split of these two species to 2.54 million years ago. We discuss additional, more recent, subdivisions within each lineage, as well as potential contact zones between the two species in the headwaters of these rivers.
Salamanders are unique among tetrapods in their ability to regenerate the limbs throughout life. Like other poikilothermic amphibians, salamanders also show a remarkable capacity to survive long periods of starvation. Whether the physiological reserves necessary for tissue regeneration are preserved or sacrificed in starved salamanders is unknown. In the current study, we maintained Iberian ribbed newts (Pleurodeles waltl) under extreme physiological stress to assess the extent of regeneration and identify the molecular and cellular changes that may occur under such conditions. After 19 months of complete food deprivation, the animals exhibited extensive morphological and physiological adaptations but remained behaviorally active and vigilant. Autophagy was elevated in different tissues and the transformed gut microbiota indicated remodeling of the intestinal tract related to autophagy. Upon limb amputation in animals starved for 21 months, regeneration proceeded with progenitor cell proliferation and migration, leading to limb blastema formation. However, limb outgrowth and patterning were substantially attenuated. Blockage of autophagy inhibited cell proliferation and blastema formation in starved animals, but not in fed animals. Hence, tissue autophagy and the regenerative response were tightly coupled only when animals were under stress. Our results demonstrate that under adverse conditions, salamanders can exploit alternative strategies to secure blastema formation for limb regeneration.
A new species of the genus Leptobrachella, Leptobrachella damingshanensis sp. nov. is described from central Guangxi, China, based on morphological, molecular, and acoustic data. Phylogenetic analyses using a 16S rRNA gene fragment indicated that the new species formed an independent clade close to L. nahangensis and L. nyx. However, the new species differs from all known congeners based on a combination of the following characters: medium size (snout-vent length (SVL) 33.6–34.4 mm in males); pair of distinct jacinth humeral glands on proximal thigh area; rough dorsal skin with sparse jacinth tubercles and several short longitudinal ridges; creamy white ventral surface with small, creamy white glands on throat, chest, belly, and ventral surfaces of thighs, becoming more concentrated near lateral margin; webbing and lateral fringes absent on fingers, toes with rudimentary webbing and narrow lateral fringes; flanks with small irregular black spots; iris bicolored, upper half copper, fading to silver in lower half. Uncorrected p-distances were greater than 4.7% between Leptobrachella damingshanensis sp. nov. and all homologous DNA sequences available for the 16S rRNA gene. The new species is only known to occur in the Damingshan National Nature Reserve, where it inhabits montane evergreen forests between 1 000–1 200 m a.s.l.
Although it first appeared almost two years ago, the COVID-19 pandemic continues to have an impact on a global scale, in part due to newly emerging SARS-CoV-2 variants such as Delta and Lambda. The B.1.621 variant, first identified in Colombia in January 2021, was classified as a variant of interest (VOI) and designated as Mu by the World Health Organization (WHO) in August 2021. However, its infectivity and resistance to neutralizing antibodies remain largely unknown. Here, in comparison to Delta, the Mu variant showed an unexpectedly enhanced immune resistance to inactivated vaccine-elicited antibodies. Nevertheless, Mu demonstrated less infectivity than Delta, implying a biological trade-off between viral transmission and immune escape. This study strongly calls for urgent evaluation of the protective efficacy of current COVID-19 vaccines against the Mu variant.
Ectatosticta spiders from the Qinghai-Tibet Plateau were studied. Multilocus molecular and morphological data identified 16 putative species, including seven new species: Ectatosticta wenshu Lin & S. Li sp. nov. , Ectatosticta baima Lin & S. Li sp. nov. , Ectatosticta helii Lin & S. Li sp. nov. , Ectatosticta shaseng Lin & S. Li sp. nov. , Ectatosticta puxian Lin & S. Li sp. nov. , Ectatosticta qingshi Lin & S. Li sp. nov. , and Ectatosticta baixiang Lin & S. Li sp. nov. This increase in the number of Ectatosticta species from a single species in 2008 to 16 in the current study highlights the Linnean shortfall in China. The previously known distribution of Ectatosticta spiders was from one locality in Shaanxi and is now expanded to the east and south of the Qinghai-Tibet Plateau.
In the present study, we successfully assembled a high-quality genome of Planiliza haematocheila (redlip mullet) based on Oxford Nanopore long read, single-tube long fragment read (stLFR), and Hi-C chromatin interaction sequencing. The size of the P. haematocheila genome was 652.91 Mb. More than 93.8% of BUSCO genes were detected, and the N50 lengths of contigs and scaffolds reached 7.21 Mb and 28.01 Mb, respectively, thus demonstrating outstanding genome completeness and sequence continuity. A total of 21 045 protein-coding genes were predicted in the assembled genome, and 99.77% of those genes were functionally annotated. Comparative genomic and phylogenetic analyses revealed the adaptability of P. haematocheila to complex living environments at the genomic level, highlighting its broad adaptability and resistance to multiple stresses as an important economic fish. The high-quality reference chromosome-level genome of P. haematocheila provides a powerful genomic resource for further systematic study of Mugilidae.
Autism spectrum disorder (ASD) is typically characterized by common deficits in social skills and repetitive/stereotyped behaviors. It is widely accepted that genetic and environmental factors solely or in combination cause ASD. However, the underlying pathogenic mechanism is unclear due to its highly heterogeneous nature. To better understand the pathogenesis of ASD, various animal models have been generated, which can be generally divided into genetic, environment-induced, and idiopathic animal models. In this review, we summarize the common animals used for ASD study and then discuss the applications, clinical insights, as well as challenges and prospects of current ASD animal models.
As a top predator, the Eurasian otter (Lutra lutra) is an indicator of healthy freshwater ecosystems and a flagship species for conservation. Once widespread in China, the species is now distributed mainly in the upper reaches of the great rivers of western China. However, a lack of knowledge on local otter populations continues to hinder their conservation in China. Here, we conducted a detailed study on habitat use of Eurasian otters in Yushu City and Tangjiahe National Nature Reserve in western China using transect surveys. At both study sites, otters preferred to defecate on large rocks close to or protruding from the river and about 50 cm above the waterline. In Yushu, no spraints were found along the 5 km river bank section in the downtown area, with otters preferring sprainting sites with natural banks, riparian zones, and lower human population density. However, this pattern was not obvious at Tangjiahe, where river transformation and human disturbance are minor. Otter river use intensity was negatively correlated with elevation and human population density in Yushu in both seasons. In Tangjiahe, otter river use intensity was positively correlated with prey mass and flow rate and negatively correlated with human population in spring, but positively correlated with human population and negatively correlated with flow rate in autumn. These results reflect the flexible habitat use strategies of otters at different sites, underlining the necessity to study otters living in different regions and habitat types. We provide suggestions for river modification and call for more site-specific studies to promote otter conservation in China.
Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four Manis javanica and, for the first time, one M. pentadactyla. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22895 bp (MP20) from the M. pentadactyla sample. Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M. javanica seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.
2021, 42(6): 845-845.