Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini

The insect mitogenome is typically a compact circular molecule with highly conserved gene contents.Nonetheless,mitogenome structural variations have been reported in specific taxa,and gene rearrangements,usually the tRNAs,occur in different lineages.Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences,comparative analyses of mitogenomes have been given increasing attention.However,most studies use a very few species to represent the whole genus,tribe,family,or even order,overlooking potential variations at lower taxonomic levels,which might lead to some incorrect inferences.To provide new insights into mitogenome organizations and their implications for phylogenetic inference,this study conducted comparative analyses for mitogenomes of three social bee tribes(Meliponini,Bombini,and Apini)based on the phylogenetic framework with denser taxonomic sampling at the species and population levels.Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type,while those of Meliponini show diverse variations in mitogenome sizes and organizations.Large inverted repeats(IRs)cause significant gene rearrangements of protein coding genes(PCGs)and rRNAs in Indo-Malay/Australian stingless bee species.Molecular evolution analyses showed that the lineage with IRs have lower dN/dS ratios for PCGs than lineages without IRs,indicating potential effects of IRs on the evolution of mitochondrial genes.The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution.Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini,tRNA rearrangements are common across all three tribes of social bees,and are significant even at the species level,indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements,and their implications for phylogenetic inference.

香港乡土树种幼苗在次生林下生长的研究(英文)

通过苗木移植试验，测定了２１种香港乡土树种在次生林下的成活率及生长状况．结果表明，大多数种类的幼苗具有一定的耐荫性，可在林下生长；只有极少数种类表现出极耐荫或极不耐荫，导致林下先锋树种幼苗死亡率高的主要原因是荫蔽或因荫蔽而生长不良受病虫害致死．在香港次生林演替中占优势的种类通常具有生长快、稍耐荫，或生长稍慢但耐胁迫等特点．这是对香港退化土地长期适应的结果．鸟播植物在香港次生林中占有重要地位，建议加强鸟播树种生态学特性的研究及其在植树造林中应用．结合本实验结果，对一些现代植物群落演替假说进行了简要的讨论．

香港次生林树种种子生理生态学特性的研究

１９８９～１９９１年在温室和野外测定了香港４０种次生林树木种类的种子寿命和发芽率．结果显示，在所测试的４０种天然林树种中，６０％的树种的种子寿命短于１年，仅有８个树种的种子寿命在１年以上．种子的寿命与种子在土壤中的发芽能力呈负相关的关系．种子发芽测定结果表明，大多数树种都可以在强光照条件（９５％的日光）下发芽，但３５％的测试树种不能在天然林下（０７％～２％的日光）发芽．最后从植物生理生态的角度。

Decoding the evolution and transmissions of the novel pneumonia coronavirus(SARS-CoV-2/HCoV-19)using whole genomic data

The outbreak of COVID-19 started in mid-December2019 in Wuhan, China. Up to 29 February 2020,SARS-CoV-2(HCoV-19/2019-nCoV) had infected more than 85 000 people in the world. In this study,we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak.We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau(τ)using the formula t=τ/2 u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes.Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes(31 found in samples from China and 31 from outside China)were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome(bat-RaTG13-CoV)as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes,and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore,phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.

Safeguarding our future by protecting biodiversity

The Anthropocene is marked by twin crises:climate change and biodiversity loss.Climate change has tended to dominate the headlines,reflecting,in part,the greater complexity of the biodiversity crisis.Biodiversity itself is a difficult concept.Land plants dominate the global biomass and terrestrial arthropods probably dominate in terms of numbers of species,but most of the Tree of Life consists of single-celled eukaryotes,bacteria,and archaea.Wild plants provide a huge variety of products and services to people,ranging from those that are species-specific,such as food,medicine,and genetic resources,to many which are partly interchangeable,such as timber and forage for domestic animals,and others which depend on the whole community,but not on individual species,such as regulation of water supply and carbon sequestration.The use of information from remote sensing has encouraged a simplified view of the values of nature's contributions to people,but this does not match the way most people value nature.We can currently estimate the proportion of species threatened by human impacts only for a few well-assessed groups,for which it ranges from 14%(birds)to 63%(cycads).Less than 8%of land plants have been assessed,but it has been estimated that 30e44%are threatened,although there are still few(0.2%)well-documented extinctions.Priorities for improving protection of biodiversity include:improving the inventory,with surveys focused on geographical areas and taxonomic groups which are under-collected;expanding the protected area system and its representativeness;controlling overexploitation;managing invasive species;conserving threatened species ex situ;restoring degraded ecosystems;and controlling climate change.The Convention on Biological Diversity(CBD)COP15 and the United Nations Framework Convention on Climate Change(UNFCCC)COP26 meetings,both postponed to 2021,will provide an opportunity to address both crises,but success will require high ambition from all participants.

Road induced edge effects on a forest bird community in tropical Asia

Background: Edge effects cause changes in bird community richness, abundance, and/or distribution within a landscape, but the avian guilds most influenced can vary among regions. Although Southeast Asia has the highest rates of deforestation and projected species loss, and is currently undergoing an explosive growth in road infrastructure, there have been few studies of the effects of forest edges on avian communities in this region.Methods: We examined avian community structure in a dry evergreen forest in northeastern Thailand adjacent to a five-lane highway. We evaluated the richness and abundance of birds in 11 guilds at 24 survey points on three parallel transects perpendicular to the edge. At each point, 10-min surveys were conducted during February-August 2014 and March-August 2015. Vegetation measurements were conducted at 16 of the bird survey points and ambient noise was measured at all 24 survey points.Results: We found a strongly negative response to the forest edge for bark-gleaning, sallying, terrestrial, and understory insectivores and a weakly negative response for arboreal frugivore-insectivores, foliage gleaning insectivores, and raptors. Densities of trees and the percentage canopy cover were higher in the interior, and the ambient noise was lower. In contrast, arboreal nectarivore-insectivores responded positively to the forest edge, where there was a higher vegetation cover in the ground layer, a lower tree density, and a higher level of ambient noise.Conclusion: Planners should avoid road development in forests of high conservation value to reduce impacts on biodiversity. Where avoidance is impossible, a number of potential mitigation methods are available, but more detailed assessments of these are needed before they are applied in this region.

环境DNA技术及其应用

近年来,人类活动影响导致水生态系统遭到破坏,水生生物多样性锐减,水生态功能严重退化并影响人类健康。而生物多样性是维持生态平衡的基础,因此,对水生生物进行监测是开展水生态环境管理和保护的前提。目前,传统的水生态研究主要依赖形态学生物监测,以及通过直接观察、显微镜和生物声学收集数据。然而传统形态学生物监测存在费时费力、成本高、物种分辨度低等诸多缺陷,无法在流域开展大规模、高频率的水生态监测。

Genomic variation,environmental adaptation,and feralization in ramie,an ancient fiber crop

Feralization is an important evolutionary process,but the mechanisms behind it remain poorly understood.Here,we use the ancient fiber crop ramie(Boehmeria nivea(L.)Gaudich.)as a model to investigate genomic changes associated with both domestication and feralization.We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes.Next,we gathered 915 accessions from 23 countries,comprising cultivars,major landraces,feral populations,and the wild progenitor.Based on whole-genome resequencing of these accessions,we constructed the most comprehensive ramie genomic variation map to date.Phylogenetic,demographic,and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin,i.e.,descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces.Feral ramie has higher genetic diversity than wild or domesticated ramie,and genomic regions affected by natural selection during feralization differ from those under selection during domestication.Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor,and three environmental variables are associated with habitat-specific adaptation in feral ramie.These findings advance our understanding of feralization,providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Plant diversity in a changing world: status,trends,and conservation needs

The conservation of plants has not generated the sense of urgency—or the funding—that drives the conservation of animals,although plants are far more important for us. There are an estimated 500,000 species of land plants( angiosperms,gymnosperms,ferns,lycophytes,and bryophytes),with diversity strongly concentrated in the humid tropics. Many species are still unknown to science. Perhaps a third of all land plants are at risk of extinction,including many that are undescribed,or are described but otherwise data deficient. There have been few known global extinctions so far,but many additional species have not been recorded recently and may be extinct. Although only a minority of plant species have a specific human use,many more play important roles in natural ecosystems and the services they provide,and rare species are more likely to have unusual traits that could be useful in the future. The major threats to plant diversity include habitat loss,fragmentation,and degradation,overexploitation,invasive species,pollution,and anthropogenic climate change. Conservation of plant diversity is a massive task if viewed globally,but the combination of a well-designed and well-managed protected area system and ex situ gap-filling and back-up should work anywhere. The most urgent needs are for the completion of the global botanical inventory and an assessment of the conservation status of the 94% of plant species not yet evaluated,so that both in and ex situ conservation can be targeted efficiently.Globally,the biggest conservation gap is in the hyperdiverse lowland tropics and this is where attention needs to be focused.

A short note on seed dispersal by colobines:the case of the proboscis monkey

Although the role of primates in seed dispersal is generally well recognized,this is not the case for colobines,which are widely distributed in Asian and African tropical forests.Colobines consume leaves,seeds and fruits,usually unripe.A group of proboscis monkeys(Colobinae,Nasalis larvatus)consisting of 1 alpha-male,6 adult females and several immatures,was observed from May 2005 to May 2006.A total of 400 fecal samples from focal group members covering 13 months were examined,with over 3500 h of focal observation data on the group members in a forest along the Menanggul River,Sabah,Malaysia.Intact small seeds were only found in 23 of 71 samples in Nov 2005,15 of 38 in Dec 2005 and 5 of 21 in Mar 2006.Seeds of Ficus(all<1.5 mm in length)were found in all 3 months and seeds from Antidesma thwaitesianum(all<3 mm)and Nauclea subdita(all<2 mm)only in Nov and Dec,which was consistent with members of the study group consuming fruits of these species mostly at these times.To our knowledge,these are the fi rst records of seeds in the fecal samples of colobines.Even if colobines pass relatively few seeds intact,their high abundance and biomass could make them quantitatively significant in seed dispersal.The potential role of colobines as seed dispersers should be considered by colobine researchers.

Winners and losers among tree species in Xishuangbanna: which traits are most important?

Massive human interference in natural ecosystems is resulting in a few ＂winners＂ and many ＂losers＂. However, the drivers of this winner-loser replacement pattern remain poorly understood. The aim of the study reported here was to identify winners among the tree flora of Xishuangbanna and compare their functional traits, specific leaf area （SLA）, wood density （WD）, seed mass （SM） and maximum height （MH） with previously identified losers （i.e., endangered species）. Fifteen native tree species were identified as winners from expert opinion, plot-based surveys of secondary forests and plotless surveys along roads. Twelve endangered tree species for which trait information could be obtained were used for comparison. Traits were compared with a Wilcoxon rank-sum test. Winners had significantly higher SLA, but lower WD. SM and MH did not differ significantly between groups. When the effects of phylogeny were removed by using phylogenetic generalized least squares, the difference in SLA became marginally insignificant. Principal component analysis resulted in two overlapping groups, showing that the selected traits were insufficient to distinguish winners and losers. Our results suggest that the ＂few winners, many losers＂ paradigm applies to trees in Xishuangbanna, with15 species accounting for most trees in the disturbed habitats sampled.

Seed dispersal in Hong Kong,China:past,present and possible futures

In the present article,published and unpublished information regarding seed dispersal in the degraded landscape of Hong Kong,China,is reviewed.Information was available for 1681 native plant species,of which 1165 were assigned to probable seed dispersal modes.Endozoochory accounted for one-third(34.4%)of all species evaluated,half(54.4%)of those from forests,and more than two-thirds(69.2%)of all trees and tall shrubs.Wind dispersal(25.9%)and dispersal by an unknown agent(30.7%)accounted for most of the rest,with the unknown species mostly small-seeded herbs.Although the frugivore fauna of the Hong Kong region has been truncated since the late Pleistocene,there are few clear examples of failed mutualisms.The most striking is the absence of scatter-hoarding rodents from Hong Kong,despite the presence of forest trees that appear to require them for effective dispersal.There are also some large Lauraceae fruits that appear to be targeted at larger-gaped birds than currently present.Most endozoochorous species are dispersed by 3 small passerine birds(Pycnonotus jocosus,P.sinensis,and Zosterops japonicus),with larger birds,fruit bats(Cynopterus sphinx,Rousettus leschenaulti),rhesus macaques(Macaca mulatta),civets(Paguma larvata,Viverricula indica),and muntjacs(Muntiacus muntjac)accounting for the remainder.The low plant diversity in frugivore droppings,seed traps,and secondary vegetation suggests plant succession may be dispersal limited,although this has not been investigated experimentally.Planting underdispersed species is the simplest solution but,in the longer term,the(re)introduction of a scatter-hoarding rodent should be considered as well as that of other locally and regionally extinct frugivores.

The potential for biochar application in rubber plantations in Xishuangbanna,Southwest China:a pot trial

Biochar can enhance crop production and sequester carbon,but there have been few studies with tree crops.Rubber plantations cover more than 8 million hectares in Southeast Asia,so we assessed the feasibility of biochar application in these plantations with a pot trial.Rubber seedlings were planted in soil with four concentrations(0,1.25%,2.5% and 5%,w/w)of biochar combined with two concentrations of compound fertilizer(0 kg/ha and 300 kg/ha).Soil properties and seedling growth were measured,and a leaching experiment was conducted in the rainy season.Our results show that biochar increased pH,water content(27.4-65.1%),total carbon(25.4-53.6%),nitrate nitrogen,and available phosphorus in the soil,and decreased bulk density(3.2-23.9%).Biochar treatment reduced leaching of ammonium nitrogen and ortho-P.Biochar increased seedling nutrient uptake(C,N,P and K),with 2.5% and 5% biochar showing the largest effects,but seedling biomass was the highest with 1.25%,and declined in 2.5% and 5%.Our results suggest that biochar addition is an effective way to improve rubber plantation soils,sequester more carbon and decrease nutrient leaching,but the optimum application rate under field conditions needs further research.