Genetic mechanisms of animal camouflage: an interdisciplinary perspective.

Camouflage is a classic example of a trait wherein animals respond to natural selection to avoid predation or attract prey. This unique phenomenon has attracted significant recent attention and the rapid development of integrative research methods is facilitating advances in our understanding of the in-depth genetic mechanisms of camouflage. In this review article, we revisit camouflage definitions and strategies and then we examine the underlying mechanisms of the two most common forms of camouflage, crypsis and masquerade, that have recently been elucidated using multiple approaches. We also discuss unresolved questions related to camouflage. Ultimately, we highlight the implications of camouflage for informing various key issues in ecology and evolution.

Gut microbiome as a key monitoring indicator for reintroductions of captive animals.

Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild.

Microbiomas intestinales como indicadores clave de monitoreo para la reintroducción de animales cautivos Resumen Los programas de reintroducción buscan restaurar las poblaciones degradadas y revertir la pérdida de la biodiversidad. Realizamos un monitoreo metagenómico intensivo durante más de diez años para caracterizar la sucesión ecológica y la evolución adaptativa de los simbiontes intestinales de pandas reintroducidos en la naturaleza y así comprobar la hipótesis de que estos simbiontes pueden usarse como indicadores de una reintroducción exitosa. Recolectamos 63 muestras fecales de tres individuos reintroducidos y 22 de nueve individuos silvestres y usamos 96 muestras disponibles al público de otros tres individuos cautivos. Mediante el análisis de la composición microbiana identificamos tres grupos comunitarios del microbioma intestinal (denominados como enterotipos) con una sucesión entre enterotipos relacionada cercanamente al proceso de reintroducción. Identificamos cada uno de los tres enterotipos con base en la variación significativa en los niveles de uno de los tres géneros: Clostridium, Pseudomonas, y Escherichia. El enterotipo de los pandas cautivos fue Escherichia. A este enterotipo lo reemplazó gradualmente el enterotipo de Clostridium durante el proceso de adaptación a la naturaleza, y a su vez fue reemplazado por el enterotipo de Pseudomonas similar al de los pandas silvestres, un indicador de la conversión a la vida silvestre y de una reintroducción exitosa. También aislamos una cepa de Pseudomonas protegens del enterotipo silvestre, un microbio reportado previamente como de vida libre, y descubrimos que su evolución dentro del hospedero contribuyó a que este se adaptara a la naturaleza de la dieta. El monitoreo de la estructura microbiana intestinal proporciona una herramienta novedosa y no invasiva que puede usarse como indicador del éxito de la reintroducción de un individuo cautivo a la naturaleza.

PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation.

BACKGROUND: The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS: The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS: Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.

Evolutionary genomics of camouflage innovation in the orchid mantis.

The orchid mantises achieve camouflage with morphological modifications in body color and pattern, providing an interesting model for understanding phenotypic innovation. However, a reference genome is lacking for the order Mantodea. To unveil the mechanisms of plant-mimicking body coloration and patterns, we performed de novo assembly of two chromosome-level genomes of the orchid mantis and its close relative, the dead leaf mantis. Comparative genomic analysis revealed that the Scarlet gene plays an important role in the synthesis of xanthommatin, an important pigment for mantis camouflage coloration. Combining developmental transcriptomic analysis and genetic engineering experiments, we found that the cuticle was an essential component of the 'petal-like' enlargement, and specific expression in the ventral femur was controlled by Wnt signaling. The prolonged expression of Ultrabithorax (Ubx) accompanied by femoral expansion suggested that Ubx determines leg remodeling in the early developmental stage. We also found evidence of evolution of the Trypsin gene family for insectivory adaptation and ecdysone-dependent sexual dimorphism in body size. Overall, our study presents new genome catalogs and reveals the genetic and evolutionary mechanisms underlying the unique camouflage of the praying mantis, providing evolutionary developmental insights into phenotypic innovation and adaptation.

Influence of Last Glacial Maximum legacies on functional diversity and community assembly of extant Chinese terrestrial vertebrates.

Contemporary biodiversity patterns are shaped by not only modern climate but also factors such as past climate fluctuations. Investigating the relative degree of paleoclimate legacy could help us understand the formation of current biodiversity patterns. However, an assessment of this issue in China is lacking. Here, we investigated the phylogenetic structure and functional diversity patterns of Chinese terrestrial vertebrates. We found that Southern China harbored higher functional richness, while Northern and Western China were more phylogenetically clustered with higher functional divergence and evenness, indicating environmental filtering effects. Moreover, we found that drastic Last Glacial Maximum climate changes were positively related to phylogenetic clustering, lower functional richness, and higher functional divergence and evenness, although this effect varied among different taxonomic groups. We further found that mammal communities experiencing more drastic Last Glacial Maximum temperature changes were characterized by "faster" life-history trait values. Our findings provide new evidence of the paleoclimate change legacies influencing contemporary biodiversity patterns that will help guide national-level conservation plans.

Global patterns of phylogenetic diversity and transmission of bat coronavirus.

Bats are reservoirs for multiple coronaviruses (CoVs). However, the phylogenetic diversity and transmission of global bat-borne CoVs remain poorly understood. Here, we performed a Bayesian phylogeographic analysis based on 3,594 bat CoV RdRp gene sequences to study the phylogenetic diversity and transmission of bat-borne CoVs and the underlying driving factors. We found that host-switching events occurred more frequently for α-CoVs than for ß-CoVs, and the latter was highly constrained by bat phylogeny. Bat species in the families Molossidae, Rhinolophidae, Miniopteridae, and Vespertilionidae had larger contributions to the cross-species transmission of bat CoVs. Regions of eastern and southern Africa, southern South America, Western Europe, and Southeast Asia were more frequently involved in cross-region transmission events of bat CoVs than other regions. Phylogenetic and geographic distances were the most important factors limiting CoV transmission. Bat taxa and global geographic hotspots associated with bat CoV phylogenetic diversity were identified, and bat species richness, mean annual temperature, global agricultural cropland, and human population density were strongly correlated with the phylogenetic diversity of bat CoVs. These findings provide insight into bat CoV evolution and ecological transmission among bat taxa. The identified hotspots of bat CoV evolution and transmission will guide early warnings of bat-borne CoV zoonotic diseases.

Evolutionary Conservation Genomics Reveals Recent Speciation and Local Adaptation in Threatened Takins.

Incorrect species delimitation will lead to inappropriate conservation decisions, especially for threatened species. The takin (Budorcas taxicolor) is a large artiodactyl endemic to the Himalayan-Hengduan-Qinling Mountains and is well known for its threatened status and peculiar appearance. However, the speciation, intraspecies taxonomy, evolutionary history, and adaptive evolution of this species still remain unclear, which greatly hampers its scientific conservation. Here, we de novo assembled a high-quality chromosome-level genome of takin and resequenced the genomes of 75 wild takins. Phylogenomics revealed that takin was positioned at the root of Caprinae. Population genomics based on the autosome, X chromosome, and Y chromosome SNPs and mitochondrial genomes consistently revealed the existence of two phylogenetic species and recent speciation in takins: the Himalayan takin (B. taxicolor) and the Chinese takin (B. tibetana), with the support of morphological evidence. Two genetically divergent subspecies were identified in both takin species, rejecting three previously proposed taxonomical viewpoints. Furthermore, their distribution boundaries were determined, suggesting that large rivers play important roles in shaping the genetic partition. Compared with the other subspecies, the Qinling subspecies presented the lowest genomic diversity, higher linkage disequilibrium, inbreeding, and genetic load, thus is in urgent need of genetic management and protection. Moreover, coat color gene (PMEL) variation may be responsible for the adaptive coat color difference between the two species following Gloger's rule. Our findings provide novel insights into the recent speciation, local adaptation, scientific conservation of takins, and biogeography of the Himalaya-Hengduan biodiversity hotspot.

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates.

Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to ß-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.

Integrated index-based assessment reveals long-term conservation progress in implementation of Convention on Biological Diversity.

The Convention on Biological Diversity (CBD) has launched two long-term, target-based conservation Strategic Plans in the past two decades. We compiled an index-based assessment framework to evaluate target achievements of the CBD using long-term indicators. The CBD Index is steadily increasing, with the Goal Indices for biodiversity mainstreaming, protection, and supporting mechanisms all improving over time. While the State and Pressure Indices continue to deteriorate coupled with human population and economic development, their changing rates have slowed down, most likely because of the constantly growing conservation efforts as revealed by the Response Index. The first quantitative assessment of the CBD's long-term performance may provide critical science-based evidence for continuing commitments to developing and implementing a new Post-2020 Global Biodiversity Framework. We also call for enhanced efforts to address the emerging challenges in achieving the 2050 Vision for Biodiversity and the adoption of a rapid assessment framework to track future progress.

Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda.

Characteristics of the gut microbiome vary synchronously with changes in host diet. However, the underlying effects of these fluctuations remain unclear. Here, we performed fecal microbiota transplantation (FMT) of diet-specific feces from an endangered mammal (the giant panda) into a germ-free mouse model. We demonstrated that the butyrate-producing bacterium Clostridium butyricum was more abundant during shoot-eating season than during the leaf-eating season, congruent with the significant increase in host body mass. Following season-specific FMT, the microbiota of the mouse model resembled that of the donor, and mice transplanted with the microbiota from the shoot-eating season grew faster and stored more fat. Mechanistic investigations revealed that butyrate extended the upregulation of hepatic circadian gene Per2, subsequently increasing phospholipid biosynthesis. Validation experiments further confirmed this causal relationship. This study demonstrated that seasonal shifts in the gut microbiome affect growth performance, facilitating a deeper understanding of host-microbe interactions in wild mammals.

Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer.

Muntjac deer have experienced drastic karyotype changes during their speciation, making it an ideal model for studying mechanisms and functional consequences of mammalian chromosome evolution. Here we generated chromosome-level genomes for Hydropotes inermis (2n = 70), Muntiacus reevesi (2n = 46), female and male M. crinifrons (2n = 8/9) and a contig-level genome for M. gongshanensis (2n = 8/9). These high-quality genomes combined with Hi-C data allowed us to reveal the evolution of 3D chromatin architectures during mammalian chromosome evolution. We find that the chromosome fusion events of muntjac species did not alter the A/B compartment structure and topologically associated domains near the fusion sites, but new chromatin interactions were gradually established across the fusion sites. The recently borne neo-Y chromosome of M. crinifrons, which underwent male-specific inversions, has dramatically restructured chromatin compartments, recapitulating the early evolution of canonical mammalian Y chromosomes. We also reveal that a complex structure containing unique centromeric satellite, truncated telomeric and palindrome repeats might have mediated muntjacs' recurrent chromosome fusions. These results provide insights into the recurrent chromosome tandem fusion in muntjacs, early evolution of mammalian sex chromosomes, and reveal how chromosome rearrangements can reshape the 3D chromatin regulatory conformations during species evolution.

Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal.

BACKGROUND: Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap. RESULTS: Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species. CONCLUSIONS: Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.

Morphological and Phylogenetic Analysis of Eustrongylides sp. and Gnathostoma spinigerum Parasitizing the Asian Swamp Eel Monopterusalbus in China.

Nematode infections transmitted to humans by the consumption of wild or cultured eels are increasingly being reported. In the present study, 120 Asian swamp eel, Monopterus albus (Zuiew), individuals collected from China were examined for parasite infections, and 78 larval nematodes were isolated. Morphological and molecular characteristics, including sequence and phylogenetic analysis of the internal transcribed spacer (ITS) and cytochrome c oxidase subunit I (COI) gene regions, were employed to identify these nematodes at the lowest taxonomic level possible. Asian swamp eel was infected with two zoonotic parasite taxa: Gnathostoma spinigerum advanced third-stage larvae, with 6.67% prevalence and mean intensity = 1.25, and Eustrongylides sp. fourth-stage larvae, with 26.67% prevalence and mean intensity = 2.13. These findings evidence the need to enhance public hygiene and food safety awareness toward eel consumption.

Extracellular vesicles derived from mesenchymal stem cells containing microRNA-381 protect against spinal cord injury in a rat model via the BRD4/WNT5A axis.

AIMS: Non-coding microRNA (miRNA) in extracellular vesicles (EVs) derived from mesenchymal stem cells (MSCs) may promote neuronal repair after spinal cord injury (SCI). In this paper we report on the effects of MSC-EV-microRNA-381 (miR-381) in a rodent model of SCI. METHODS: In the current study, the luciferase assay confirmed a binding site of bromodomain-containing protein 4 (BRD4) and Wnt family member 5A (WNT5A). Then we detected expression of miR-381, BRD4, and WNT5A in dorsal root ganglia (DRG) cells treated with MSC-isolated EVs and measured neuron apoptosis in culture by terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining. A rat model of SCI was established to detect the in vivo effect of miR-381 and MSC-EVs on SCI. RESULTS: We confirmed an interaction between miR-381 and BRD4, and showed that miR-381 overexpression inhibited the expression of BRD4 in DRG cells as well as the apoptosis of DRG cells through WNT5A via activation of Ras homologous A (RhoA)/Rho-kinase activity. Moreover, treatment of MSC-EVs rescued neuron apoptosis and promoted the recovery of SCI through inhibition of the BRD4/WNT5A axis. CONCLUSION: Taken altogether, miR-381 derived from MSC-EVs can promote the recovery of SCI through BRD4/WNT5A axis, providing a new perspective on SCI treatment. Cite this article: Bone Joint Res 2021;10(5):328-339.

Genomic Signatures of Coevolution between Nonmodel Mammals and Parasitic Roundworms.

Antagonistic coevolution between host and parasite drives species evolution. However, most of the studies only focus on parasitism adaptation and do not explore the coevolution mechanisms from the perspective of both host and parasite. Here, through the de novo sequencing and assembly of the genomes of giant panda roundworm, red panda roundworm, and lion roundworm parasitic on tiger, we investigated the genomic mechanisms of coevolution between nonmodel mammals and their parasitic roundworms and those of roundworm parasitism in general. The genome-wide phylogeny revealed that these parasitic roundworms have not phylogenetically coevolved with their hosts. The CTSZ and prolyl 4-hydroxylase subunit beta (P4HB) immunoregulatory proteins played a central role in protein interaction between mammals and parasitic roundworms. The gene tree comparison identified that seven pairs of interactive proteins had consistent phylogenetic topology, suggesting their coevolution during host-parasite interaction. These coevolutionary proteins were particularly relevant to immune response. In addition, we found that the roundworms of both pandas exhibited higher proportions of metallopeptidase genes, and some positively selected genes were highly related to their larvae's fast development. Our findings provide novel insights into the genetic mechanisms of coevolution between nonmodel mammals and parasites and offer the valuable genomic resources for scientific ascariasis prevention in both pandas.

Diet drives convergent evolution of gut microbiomes in bamboo-eating species.

Gut microbiota plays a critical role in host physiology and health. The coevolution between the host and its gut microbes facilitates animal adaptation to its specific ecological niche. Multiple factors such as host diet and phylogeny modulate the structure and function of gut microbiota. However, the relative contribution of each factor in shaping the structure of gut microbiota remains unclear. The giant (Ailuropoda melanoleuca) and red (Ailurus styani) pandas belong to different families of order Carnivora. They have evolved as obligate bamboo-feeders and can be used as a model system for studying the gut microbiome convergent evolution. Here, we compare the structure and function of gut microbiota of the two pandas with their carnivorous relatives using 16S rRNA and metagenome sequencing. We found that both panda species share more similarities in their gut microbiota structure with each other than each species shares with its carnivorous relatives. This indicates that the specialized herbivorous diet rather than host phylogeny is the dominant driver of gut microbiome convergence within Arctoidea. Metagenomic analysis revealed that the symbiotic gut microbiota of both pandas possesses a high level of starch and sucrose metabolism and vitamin B12 biosynthesis. These findings suggest a diet-driven convergence of gut microbiomes and provide new insight into host-microbiota coevolution of these endangered species.

Why wild giant pandas frequently roll in horse manure.

Attraction to feces in wild mammalian species is extremely rare. Here we introduce the horse manure rolling (HMR) behavior of wild giant pandas (Ailuropoda melanoleuca). Pandas not only frequently sniffed and wallowed in fresh horse manure, but also actively rubbed the fecal matter all over their bodies. The frequency of HMR events was highly correlated with an ambient temperature lower than 15 °C. BCP/BCPO (beta-caryophyllene/caryophyllene oxide) in fresh horse manure was found to drive HMR behavior and attenuated the cold sensitivity of mice by directly targeting and inhibiting transient receptor potential melastatin 8 (TRPM8), an archetypical cold-activated ion channel of mammals. Therefore, horse manure containing BCP/BCPO likely bestows the wild giant pandas with cold tolerance at low ambient temperatures. Together, our study described an unusual behavior, identified BCP/BCPO as chemical inhibitors of TRPM8 ion channel, and provided a plausible chemistry-auxiliary mechanism, in which animals might actively seek and utilize potential chemical resources from their habitat for temperature acclimatization.