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The common pheasant (Phasianus colchicus) in the order Galliformes and the family Phasianidae, has 30 subspecies distributed across its native range in the Palearctic realm and has been introduced to Europe, North America, and Australia. It is an important game bird often subjected to wildlife management as well as a model species to study speciation, biogeography, and local adaptation. However, the genomic resources for the common pheasant are generally lacking. We sequenced a male individual of the subspecies torquatus of the common pheasant with the Illumina HiSeq platform. We obtained 94.88 Gb of usable sequences by filtering out low-quality reads of the raw data generated. This resulted in a 1.02 Gb final assembly, which equals the estimated genome size. BUSCO analysis using chicken as a model showed that 93.3% of genes were complete. The contig N50 and scaffold N50 sizes were 178 kb and 10.2 Mb, respectively. All these indicate that we obtained a high-quality genome assembly. We annotated 16,485 protein-coding genes and 123.3 Mb (12.05% of the genome) of repetitive sequences by ab initio and homology-based prediction. Furthermore, we applied a RAD-sequencing approach for another 45 individuals of seven representative subspecies in China and identified 4,376,351 novel single nucleotide polymorphism (SNPs) markers. Using this unprecedented data set, we uncovered the geographic population structure and genetic introgression among common pheasants in China. Our results provide the first high-quality reference genome for the common pheasant and a valuable genome-wide SNP database for studying population genomics and demographic history. [ABSTRACT FROM AUTHOR]

Aims The spatial segregation hypothesis and the low-frequency hypothesis are two important proposed mechanisms that delay or prevent competitive exclusion in ecosystems. Because tree species interact with their neighbors, the importance of these potential processes can be investigated by analyzing the spatial structures of tree species. Methods The distribution of the adults of 27 common tree species in a fully mapped 5-ha subtropical forest plot in Baishanzu, eastern China, was analyzed to investigate the community-level intra- and interspecific spatial association patterns. We first tested for the overall spatial pattern in the 5- to 40-m neighborhoods and classified first-order bivariate associations with a diametric scheme based on Ripley’s K and nearest-neighbor statistic (G-function). Then heterogeneous Poisson null models were used to distinguish second-order interactions from overall spatial associations (including first-order effects). Finally, we analyzed correlations between the existence of species interactions and some attributes of the species involved. Important Findings Partial overlap and segregation increased with scale, whereas mixing decreased. Nearly 70% of the species pairs occurred less than expected at random, and only 3.4% of the species pairs were well mixed; 11.0% of all species pairs showed significant small-scale interactions, which was a greater frequency than expected by chance if species are abundant or prefer the same habitat, but less frequent than expected if species are highly aggregated. This suggests that both spatial segregation and low frequency of species facilitate species coexistence by reducing the opportunity that trees of two species encounter each other. The study also revealed that positive interactions were more prevalent than negative interactions in the forest, which indicates that positive interactions may have important effects on forest species assemblies. [ABSTRACT FROM PUBLISHER]