Interactions of Microplastics and Methane Seepage in the Deep-Sea Environment

Microplastics(MPs)are important exempla of the Anthropocene and are exerting an increasing impact on Earth’s carbon cycle.The huge imbalance between the MPs floating on the marine surface and those that are estimated to have been introduced into the ocean necessitates a detailed assessment of marine MP sinks.Here,we demonstrate that cold seep sediments,which are characterized by methane fluid seepage and a chemosynthetic ecosystem,effectively capture and accommodate small-scale(<100μm)MPs,with 16 types of MPs being detected.The abundance of MPs in the surface of the sediment is higher in methane-seepage locations than in non-seepage areas.Methane seepage is beneficial to the accumulation,fragmentation,increased diversity,and aging of MPs.In turn,the rough surfaces of MPs contribute to the sequestration of the electron acceptor ferric oxide,which is associated with the anaerobic oxidation of methane(AOM).The efficiency of the AOM determines whether the seeping methane(which has a greenhouse effect 83 times greater than that of CO_(2)over a 20-year period)can enter the atmosphere,which is important to the global methane cycle,since the deep-sea environment is regarded as the largest methane reservoir associated with natural gas hydrates.

Systematics and Species Validity of the Dabieshan Pit Viper Protobothrops dabieshanensis Huang et al. 2012: Evidence from a Mitochondrial Gene Sequence Analysis

Aimed to evaluate the phylogenetic position of the recently described Protobothrops dabieshanensis Huang et al. （2012）, phylogenic relationships of 12 species within Protobothrops based on four mtDNA gene fragments （12S RNA, 16S RNA, ND4 and Cyt b） were reconstructed in our study. The result indicates a clade composed ofP dabiesha- nensis, P. jerdonii and P xiangchengsis with strong support. The genetic distance among P dabieshanensis, P jerdonii and P xiangchengsis was much lower than other congeners. Based on the data from the phylogenetic analysis and pre- viously described morphological differences, we conclude that P dabieshanensis is a valid species with close affinities to P jerdonii and P xiangchengsis.

The Impact of Stream Landscape on Genetic Structure and Dispersal Patterns in Stream Salamander(Pachyhynobius shangchengensis)

Compared with other terrestrial environments,the stream environment generally presents a linear spatial structure and relatively simple environment.In a stream landscape,the dispersal direction of stream-type organisms usually presents a linear structure along the stream,which results in the limited dispersal and the genetic differentiation of stream-type organisms across different stream sections.The Shangcheng Stout Salamander(Pachyhynobius shangchengensis)is a narrowly distributed stream salamander in Dabie Mountains of East China.In the present study,we tested for the impact of stream landscape(i.e.waterfalls and underground river)on genetic structure and dispersal pattern in P.shangchengensis based on 12 nuclear microsatellite loci from 195 individuals in 3 populations(A,B and C)from three closely connected sections within one stream.Genetic diversity results suggested that Population B contains relatively high genetic diversity for P.shangchengensis when compared to the other populations(A and C).Detectable genetic differentiation was found(FST=0.008,P=0.007)among three populations,which was also supported by the Structure,FCA analysis and relatedness estimates of each pair of individuals among populations.The assignment test suggested that P.shangchengensis has philopatric males and female-biased dispersal(mean female Alc=.0.031,SE=0.225;mean male Alc=0.026,SE=0.198).Female-biased dispersal was also supported by analyses for each sex(i.e.Spatial autocorrelation,Genetic distance,Relatedness analysis).Our study indicated that small and isolated populations(A and C)had relatively low genetic diversity due to the limited population size.For stream salamanders,landscape features(i.e.waterfalls and underground river)can influence the ability of an individual to disperse through the landscape,and consequently influence the formation of strong genetic differentiation of P.shangchengensis.

The rough-toothed dolphin genome provides new insights into the genetic mechanism of its rough teeth

The rough-toothed dolphin(Steno bredanensis)is characterized by having teeth covered infinely wrinkled vertical ridges,which is a general manifestation of amelogenesis imperfecta.The rough surfaces are hypothesized to be an evolutionary morphological trait of feeding adaptation to increase the dolphin’s grip on prey.Here,we assembled a rough-toothed dolphin genome and performed the comparative genomic analysis to reveal the genetic basis of the special enamel.Results showed that genes related to enamel development or dental diseases have undergone diver-sified adaptive changes that may shape the special enamel morphology of this dolphin species,including positive selection(CLDN19,PRKCE,SSUH2,and WDR72),rapid evolution(LAMB3),or unique amino acid substitutions(AMTN,ENAM,MMP20,and KLK4).Meanwhile,the historical demography of rough-toothed dolphin indicated several distinct populationfluctuations associated with climate change.The genome-wide heterozygosity of this dolphin is in the middle of all published data for cetaceans.Although the population is considerable,there may be population or subspecies differentiation,and with the global warming and the increasing disturbance of human activities,we should pay more attention to protection in the future.Together,our study brings new insights into the genetic mechanisms that may have driven the evolution of the special enamel morphology in rough-toothed dolphins and provides thefirst results of genetic heterozygosity and population historical dynamics of this species,which have important guiding implications for the conservation of this dolphin species.

Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals

DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes,including gene expression regulation,transposable element repression,and genomic imprinting.However,most studies on DNA methylation have been conducted in humans and other model species,whereas the dynamics of DNA methylation across mammals remain poorly explored,limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation.Here,we generated and gathered comparative epigenomic data from 13 mammalian species,including two marsupial species,to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution.We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning,indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes.For a broader view,we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins.By analyzing the features of known and newly identified potential imprints in all studied mammals,we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors.Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution,suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory.

Seasonal and reproductive variation in chemical constituents of scent signals in wild giant pandas

Seasonally reproducing animals show many behavioral and physiological changes during the mating period, including increased signaling for intrasexual competition and mate attraction. We collected 102 anogenital gland secretions(AGS) from marking trees in Foping Nature Reserve, and used gas chromatography mass spectrometry to analyze these chemical composition. Of these marks, all but one were from males, confirmed with DNA analysis. We found that several chemical constituents, especially volatile compounds, were present only during the mating season and that the relative abundance of many compounds changed as a function of breeding season, whereas nonvolatile compounds were lower in the mating season. This seasonal variation in chemical composition of AGS most likely plays an important role in governing giant panda reproduction, including mate location, attraction, and male-male competition. The chemical properties of many of these putative chemosignals—such as volatility and longevity—are suggestive of these roles, and undoubtedly contribute to successful reproduction for this species with a characteristically sophisticated chemical communication system. We also found a number of important differences between the chemical constituents of AGS from wild pandas and those found in previous studies with captive pandas, suggesting that inappropriate chemosignal composition may contribute to poor reproductive success in captive breeding programs.

Distinctive diet-tissue isotopic discrimination factors derived from the exclusive bamboo-eating giant panda

Stable isotope analysis is very useful in animal ecology,especially in diet reconstruction and trophic studies.Differences in isotope ratios between consumers and their diet,termed discrimination factors,are essential for studies of stable isotope ecology and are species-specific and tissue-specific.Given the specialized bamboo diet and clear foraging behavior,here,we calculated discrimination factors for carbon and nitrogen isotopes from diet to tissues(tooth enamel,hair keratin and bone collagen)for the giant panda(Ailuropoda melanoleuca),a species derived from meat-eating ancestors.Our results showed that carbon discrimination factor obtained from giant panda tooth enamel(ε^(13)C_(diet-enamel)=10.0‰)and nitrogen discrimination factors from hair keratin(Δ^(15)N_(diet-hair)=2.2‰)and bone collagen(Δ^(15)N_(diet-collagen)=2.3‰)were lower,and carbon discrimination factors from hair ker­atin(Δ^(13)C_(diet-hair)=5.0‰)and bone collagen(Δ13Cdiet-collagen=6.1‰)were higher than those of other mammalian carnivores,omnivores and herbivores.Such distinctive values are likely the result of a low-nutrient and special­ized bamboo diet,carnivore-like digestive system and exceptionally low metabolism in giant pandas.

Digital Noah's Ark:last chance to save the endangered species

Global biodiversity is undergoing dramatic loss,mostly due to anthropogenic actions and climate change.Around 2.3seed plants died out each year in the past 2.5 centuries(Humphreys et al.,2019).Current species extinction rates are about 1,000 times the likely background rate of extinction(Pimm et al.,2014).

Exploring marine endosymbiosis systems with omics techniques

Endosymbiosis is the phenomenon where one organism lives inside another,usually in a mutualistic way.In this system,the hosts provide shelter and nutrients to the endosymbionts,who could affect the hosts in a physiological(Sommer and B?ckhed,2013),behavioral(Ezenwa et al.,2012),and evolutionary(Perlmutter and Bordenstein,2020)way.