Comparison of species ordinations resulting from alternative indices of interspecific association and different numbers of included species

Summary Several measures of interspecific association are compared. Dispersion and covariance are limited in value because they respond to the commonness of the species compared. Correlation is not so limited but it responds to discrepancies in commonness among the species. The practical result of these relationships between commonness and association is that only the most common species can occupy periferal positions in a species ordination. Rare species are relegated to positions near the center not on the basis of their phytosociological pattern but simply because of their rarity. Both Cole's index of association and the tetrachoric correlation overcome the problem imposed by the relationship between ordination position and species commonness and they both produce very similar results. The effect of differing numbers of species on the ordination configuration is examined using both Pearson's correlation and Cole's index. The basic pattern of the ordination is set with the first few species when Cole's index is used, however, since rare species are given more weight in the analysis with this index, the addition of several very rare species can change the configuration of the ordination.Nomenclature of species is given in Table 1.Research supported by the Eastern Deciduous Forest Biome Project, US-IBP, funded by the National Science Foundation under Interagency Agreement AG-199, BMS69-01147 A09 with the Energy Research and Development Administration — Oak Ridge National Laboratory. Research also supported by the U.S. Energy Research and Development Administration under contract with the Union Carbide Corporation. Contribution No. 240 from the EDFB, US-IBP. Publication No. 790. Environmental Sciences Division, ORNL.     

Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements

Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.     

burnr: Fire history analysis and graphics in R

We developed a new software package, burnr, for fire history analysis and plotting in the R statistical programming environment. It was developed for tree-ring fire-scar analysis, but is broadly applicable to other event analyses (e.g., avalanches, frost rings, or culturally modified trees). Our new package can read, write, and manipulate standard tree-ring fire history FHX files, produce fire—demography charts, calculate fire frequency and seasonality statistics, and run superposed epoch analysis (SEA). A key benefit of burnr is that it enables automation of analyses and plotting, especially for large data sets. The package also facilitates creative plotting, mapping, and analyses when combined with the thousands of packages available in R. In this paper, we describe the basic functionality of burnr and introduce users to fire history analyses in R.     

Radial growth of the Sahara’s oldest trees : Cupressus dupreziana A. Camus

The radial growth of Duprez’ cypress (Cupressus dupreziana A. Camus), a tree endemic to the Tassili n’Ajjer in the Central Sahara, was measured from cores taken in 1967 and 1997 from the same trees. A comparison of these cores, spanning 30 years, reveals that even in this hyper-arid climate, this species has a juvenile vigour comparable to other Mediterranean Cupressaceae. Wide individual variability was found, however, which was induced by the strong influence of microhabitat factors. Traditional dendrochronological methods of cross-dating are impossible to apply in the case of these trees. Ages of eight individuals were estimated with the help of radiocarbon dating, yielding an age range from 600 to 2400 years for trees of the most usual girths.     

Climate sensitivity of conifer growth doesn’t reveal distinct low–high dipole along the elevation gradient in the Wolong National Natural Reserve,SW China

Recent climate warming is usually hypothesized to cause tree growth decline in the semi-arid regions where forests are particularly vulnerable to warming induced increases of water deficit. But there is still a large knowledge gap of climate warming effects on tree growth of cold temperate forest in the sub-humid region. Here we assess how climate warming has affected tree growth in the Wolong National Natural Reserve, Southwestern China, where recent warming might not cause tree growth decline because of the cold-humid climatic conditions. Tree-ring data from four co-dominant coniferous species (Larix potaninii var. macrocarpa, Tsuga chinensis, Abies faxoniana and Juniperus saltuaria) along an elevation gradient (from 2700 m to 3700 m) all imprinted temperature signals, and were both positively and significantly correlated with instrumental record of temperature data during the analyzed period of 1954–2010. Furthermore, the rising temperature since 1980 induced pervasive tree growth increases and stronger temperature signals for the coniferous species along the elevation gradient. The tree-ring chronology recorded a strong coherence with instrumental temperature since 1980 and was successful to keep up with the pace of climate warming rate. If climate warming continues, further increases in forest growth could be expected, and the terrestrial carbon sink will be strengthened for the local forest ecosystem in the future.     

Genetic diversity and geographic distribution of Bemisia tabaci species complex in Nepal

Bemisia tabaci species complex comprises at least 44 cryptic species worldwide. Here, we analyze the nucleotide sequences of mitochondrial cytochrome oxidase subunit 1 (COI) gene obtained from 76 samples of B. tabaci collected from 23 districts in Nepal. This is the first genetic and geographic study of B. tabaci species complex in Nepal. Our phylogenetic study identified the presence of three cryptic species—Asia I, Asia II 1, and Asia II 5—with high interspecific but low intraspecific variations. Among the three cryptic species, Asia II 5 was the most prevalent in Nepal, constituting 64.47% of all the sequenced samples. Based on haplotype network analysis of COI sequences, Asia II 1 was more genetically diversified than the other two cryptic species. Our results provided useful information on the genetic diversity and geographic distribution of B. tabaci in Nepal, which help monitor population changes of B. tabaci at cryptic species level and develop sustainable management strategies for its control.     

Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2

SARS-CoV-2, the newly identified human coronavirus causing severe pneumonia pandemic, was probably originated from Chinese horseshoe bats. However, direct transmission of the virus from bats to humans is unlikely due to lack of direct contact, implying the existence of unknown intermediate hosts. Angiotensin converting enzyme 2 (ACE2) is the receptor of SARS-CoV-2, but only ACE2s of certain species can be utilized by SARS-CoV-2. Here, we evaluated and ranked the receptor-utilizing capability of ACE2s from various species by phylogenetic clustering and sequence alignment with the currently known ACE2s utilized by SARS-CoV-2. As a result, we predicted that SARS-CoV-2 tends to utilize ACE2s of various mammals, except murines, and some birds, such as pigeon. This prediction may help to screen the intermediate hosts of SARS-CoV-2.