Across two phylogeographic breaks: Quaternary evolutionary history of a mountain aspen (Populus rotundifolia) in the Hengduan Mountains

Biogeographical barriers to gene flow are central to plant phylogeography.In East Asia,plant distribution is greatly influenced by two phylogeographic breaks,the Mekong-Salween Divide and Tanaka-Kaiyong Line,however,few studies have investigated how these barriers affect the genetic diversity of species that are distributed across both.Here we used 14 microsatellite loci and four chloroplast DNA fragments to examine genetic diversity and distribution patterns of 49 populations of Populus rotundifolia,a species that spans both the Mekong-Salween Divide and the Tanaka-Kaiyong Line in southwestern China.Demographic and migration hypotheses were tested using coalescent-based approaches.Limited historical gene flow was observed between the western and eastern groups of P.rotundifolia,but substantial flow occurred across both the Mekong-Salween Divide and Tanaka-Kaiyong Line,manifesting in clear admixture and high genetic diversity in the central group.Wind-borne pollen and seeds may have facilitated the dispersal of P.rotundifolia following prevalent northwest winds in the spring.We also found that the Hengduan Mountains,where multiple genetic barriers were detected,acted on the whole as a barrier between the western and eastern groups of P.rotundifolia.Ecological niche modeling suggested that P.rotundifolia has undergone range expansion since the last glacial maximum,and demographic reconstruction indicated an earlier population expansion around 600 Ka.The phylogeographic pattern of P.rotundifolia reflects the interplay of biological traits,wind patterns,barriers,niche differentiation,and Quaternary climate history.This study emphasizes the need for multiple lines of evidence in understanding the Quaternary evolution of plants in topographically complex areas.

Evolutionary biogeography on Ophiocordyceps sinensis:An indicator of molecular phylogeny to geochronological and ecological exchanges

The fungus Ophiocordyceps sinensis is endemic to the vast region of the Qinghai-Tibetan plateau(QTP).The unique and complex geographical environmental conditions have led to the "sky island" distribution structure of O.sinensis.Due to limited and unbalanced sample collections,the previous data on O.sinensis regarding its genetic diversity and spatial structure have been deemed insufficient.In this study,we analyzed the diversity and phylogeographic structures of O.sinensis using internally transcribed spacer region(ITS) and 5-locus datasets by a large-scale sampling.A total of 111 haplotypes of ITS sequences were identified from 948 samples data of the fungus O.sinensis,with representing high genetic diversity,and 8 phylogenetic clades were recognized in O.sinensis.Both the southeastern Tibet and the northwestern Yunnan were the centers of genetic diversity and genetic differentiation of the fungus,and they were inferred as the glacial refugia in the Quaternary.Three distribution patterns were identified to correspond to the 8 clades,including but not limited to the coexistence of widely and specific local distributive structures.It also revealed that the differentiation pattern of O.sinensis did not fit for the isolation-by-distance model.The differentiation into the 8 clades occurred between 1.56 Myr and6.62 Myr.The ancestor of O.sinensis most likely originated in the late Miocene(6.62 Myr) in the northwestern Yunnan,and the Scene A-C of the Qinghai-Tibetan movements may have played an important role in the differentiation of O.sinensis during the late Miocene-Pliocene periods.Our current results provide a much clearer and detailed understanding of the genetic diversity and geographical spatial distribution of the endemic alpine fungus O.sinensis.It also revealed that the geochronology resulting from paleogeology could be cross-examined with biomolecular clock at a finer scale.

Comparative phylogeography of two sister species of snowcock: impacts of species-specific altitude preference and life history

Background: Phylogeographical patterns and population dynamics are usually interpreted by environmental disturbances and geographic barriers of the past. However, sister species may exhibit disparate patterns of genetic structures and population dynamics due to their habitat preference and altitude segregation. In this study, we tested how species-specific altitude habitat affected phylogeographical patterns in two sister snowcock species, Tibetan(Tetraogallus tibetanus) and Himalayan Snowcocks(T. himalayensis).Methods: A panel of seven microsatellite loci and a fragment of Mitochondrial DNA Control Region were used to investigate genetic structures and population dynamics in hope of revealing the underlying evolutionary processes through the identification of possible past demographic events.Results: Our results suggest that T. himalayensis showed a significant phylogeographical signal in mtDNA(FST microsatellite(F the glacial-interglacial cycles in the = 0.66, p < 0.001) and ST Pleistocene and followed demog= 0.11, p < 0.001) data and is stable duringraphic contraction until 0.003 million years(Mys) ago. The phylogeographical signal of T. tibetanus is lower than the level of genetic difference among populations in mtDNA(FST icrosatellite(F= 0.41, p < 0.001) and mST s been experien= 0.09, p < 0.001) data, likely benefiting from stable habitats over a long period of time. T. tibetanus hacing expansion since 0.09 Mys ago. However, an abnormally haplotype H9 from T. himalayensis clustering with T. tibetanus was spotted.Conclusion: Our results indicate that differences in habitat preference and altitude specialities were reflected in the genetic structure patterns and population dynamics of these two species. These dissimilarities in life history traits might have affected the dispersal and survival abilities of these two species differently during environmental fluctuations. The results of this study also enriched our knowledge on population differentiation and connectivity in high altitude mountain ecosystems.

Spatio-temporal history of H9N2 viruses in Iran and neighbor countries by Bayesian analysis and molecular characterization

Objective: To delineate the H9N2 influenza virus circulation within Iran and its neighboring countries, the potential source of the epidemic in these countries, and its date of origin.Methods: We obtained all hemagglutinin(HA) and neuraminidase(NA) nucleotide sequences of influenza H9N2 available up to December 25, 2020 from Iran and its neighboring countries(i.e., Pakistan, Afghanistan, Turkmenistan, Armenia, Azerbaijan, Turkey, and Iraq). We also performed a Bayesian Markov chain Monte Carlo method to infer the evolutionary dynamic and the most recent common ancestor for the HA and NA sequences.Results: H9N2 epidemic may have started in Iran and Pakistan much earlier than the other investigated countries in the region, and an ongoing bidirectional dispersion of the virus between the investigated countries was also observed. The mean time of the most recent common ancestor of H9N2 viruses was 1988 for HA, and 1992 for NA.Conclusions: Strains from investigated countries rooted in Pakistan and Iran. Regular surveillance of H9N2 viruses, especially in the live bird markets, enhancing the biosecurity of poultry industry and screening newly arriving immigrants and tourists from neighboring countries at border should be considered to control spread of the virus. Furthermore, surveillance of viral molecular evolution should be initiated for effective prevention of epidemic and pandemic spreads.

DNA-Barcoding of Some Medicinal Plant Species in Saudi Arabia Using rbcL and matK Genes

In the Kingdom of Saudi Arabia(KSA),thousands of plants are considered to have therapeutic value.The ambiguous use of identification mainly morphological characteristics of many plants has resulted in the adulteration and displacement of plant products which undermine their therapeutic value and weak documentation of plant resources.The aims of this study were therefore to evaluate genetic variability and explore the phylogeographic architecture for Saudi medicinal plant samples using rbcL and matK genes as barcodes for genomic identification.The matK and rbcL sequences collected for these samples were used as key markers for examining the relationship between Saudi medicinal plant species based on genetic diversity.During our study we were successful in identifying and documenting 4 different species(Foeniculum vulgare,Nitraria retusa,Dodonaea viscosa,and Rumex nervosus)located in Saudi Arabia using DNA barcoding technique.A total number of 8 sequences were obtained with a total sequence length of 6176 bp,where it ranged from 617 bp to 878 bp with an aver-age length of 772 bp.The total number of rbcL sequences length is 2801 bp,where it ranges from 617 bp to 807 bp with an average length of 700.2 bp.Out of the 4 plant samples used,only three samples were identified correctly on the species level with an identity percentage higher than 95%using rbcL gene.Additionally,4 matK sequences have been retrieved belong to 4 species.The total number of matK sequences length is 3375 bp,where it ranges from 819 bp to 878 bp with an average length of 843.8 bp.Out of the 4 plant samples used,only two samples were identified correctly on the species level with an identity percentage higher than 98% using matK gene.Both rbcL and matK have been able to identify most of our collected plant samples by genus,and some by species.Using only one DNA-barcoding technique was not reliable for plant identification,where matK and rbcL must be used as a dual DNA-barcoding procedure.

Population structure and genome‑wide evolutionary signatures reveal putative climate‑driven habitat change and local adaptation in the large yellow croaker

The large yellow croaker(Larimichthys crocea)is one of the most economically valuable marine fsh in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades.The stock division and species distribution,which have important implications for ecological protection,germplasm recovery,and fshery resource management,have been debated since the 1960s.However,it is still uncertain even how many stocks exist in this species.To address this,we evaluated the fne-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers.Compared with the widely accepted stock boundaries proposed in the 1960s,our results revealed that a climate-driven habitat change probably occurred between the Naozhou(Nanhai)Stock and the Ming-Yuedong(Mindong)Stock.The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait,accompanied by highly asymmetric introgression.In addition,we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas.The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes,whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations.These fndings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker,providing a basis for conservation,fsheries management and further evolutionary biology studies.

The potential drivers in forming avian biodiversity hotspots in the East Himalaya Mountains of Southwest China

Little has been published to describe or interpret Asian biodiversity hotspots,including those in the East Himalayan Mountains of Southwest China(HMSC),thus making necessary a review of the current knowledge.The Pliocene and Pleistocene geological and glacial histories of the Asian continent differ from those of Europe and North America,suggesting different mechanisms of speciation and extinction,and,thus,different responses to climate changes during the Quaternary glaciations.This short review summarizes potential drivers in shaping and maintaining high species richness and endemism of birds in the HMSC.The geographical location at the junction of different biogeographical realms,the wide range of habitats and climates along the extensive elevational range,the complex topography and the distinct geological history of this region have probably contributed to the evolution of an exceptionally species-rich and endemic-rich,specialized montane avian fauna.The Mountain systems in the HMSC may have provided refugia where species survived during the glacial periods and barriers for preventing species dispersal after the glacial periods.More studies are required to further test this refugia hypothesis by comparing more cold-tolerent and warm-tolerent species.

Epidemiology and evolution of Middle East respiratory syndrome coronavirus, 2012-2020

Background:The ongoing transmission of the Middle East respiratory syndrome coronavirus(MERS-CoV)in the Middle East and its expansion to other regions are raising concerns of a potential pandemic.An in-depth analysis about both population and molecular epidemiology of this pathogen is needed.Methods:MERS cases reported globally as of June 2020 were collected mainly from World Health Organization official reports,supplemented by other reliable sources.Determinants for case fatality and spatial diffusion of MERS were assessed with Logistic regressions and Cox proportional hazard models,respectively.Phylogenetic and phylogeographic analyses were performed to examine the evolution and migration history of MERS-CoV.Results:A total of 2562 confirmed MERS cases with 150 case clusters were reported with a case fatality rate of 32.7%(95%Cl:30.9-34.6%).Saudi Arabia accounted for 83.6%of the cases.Age of>65 years old,underlying conditions and>5 days delay in diagnosis were independent risk factors for death.However,a history of animal contact was associated with a higher risk(adjusted OR=297,95%Cl:1」0-7.98)among female cases<65 years but with a lower risk(adjusted OR=0.31,95%Cl:0.18-0.51)among male cases>65 years old.Diffusion of the disease was fastest from its origin in Saudi Arabia to the east,and was primarily driven by the transportation network.The most recent subclade C5.1(since 2013)was associated with non-synonymous mutations and a higher mortality rate.Phylogeographic analyses pointed to Riyadh of Saudi Arabia and Abu Dhabi of the United Arab Emirates as the hubs for both local and international spread of MERS-CoV.Conclusions:MERS-CoV remains primarily locally transmitted in the Middle East,with opportunistic exportation to other continents and a potential of causing transmission clusters of human cases.Animal contact is associated with a higher risk of death,but the association differs by age and sex.Transportation network is the leading driver for the spatial diffusion ofthe disease.These findings how this pathogen spread are helpful for targeting public health surveillance and interventions to control endemics and to prevent a potential pandemic.

Spatial, Temporal and Genetic Dynamics Characteristics of Influenza B Viruses in China, 1973–2018

Annual influenza B virus epidemics and outbreaks cause severe influenza diseases in humans and pose a threat to public health. China is an important epidemic area of influenza B viruses. However, the spatial, temporal transmission pathways and the demography history of influenza B viruses in China remain unknown. We collected the haemagglutinin gene sequences sampled of influenza B virus in China between 1973 and 2018. A Bayesian Markov chain Monte Carlo phylogeographic discrete approach was used to infer the spatial and temporal phylodynamics of influenza B virus. The Bayesian phylogeographic analysis of influenza B viruses showed that the North subtropical and South subtropical zones are the origins of the Victoria and Yamagata lineage viruses, respectively. Furthermore, the South temperate and North subtropical zones acted as transition nodes in the Victoria lineage virus dispersion network and that the North subtropical and Mid subtropical zones acted as transition nodes in the Yamagata lineage virus dispersion network. Our findings contribute to the knowledge regarding the spatial and temporal patterns of influenza B virus outbreaks in China.