Genome Assembly of the Common Pheasant Phasianus colchicus: A Model for Speciation and Ecological Genomics

A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics

The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.

The screening method for use of wild pheasant feathers in the monitoring of environmental pollution with heavy metals

It has been shown that some species of birds, especially herbivorous and territorial ones, are more sensitive to the effects of toxic substances compared to mammals. This allows for taking integrated actions in the area of environmental protection and monitoring in a holistic sense (at various trophic levels). Therefore, this study aimed to assess the possibility of using pheasant feathers (Phasianus colchicus) as a potential bioindicator ofenvironmental contamination, and thus to determine the concentration of heavy metals (lead-Pb, arsenic-As, cadmium-Cd, chromium-Cr, nickel-Ni, and zinc-Zn) in the analyzed tissue of animals inhabiting the forest districts of the Lubartów, Tomaszów, Skierniewice, and Ostrowiec Świętokrzyski areas. The chemical analysis used to determine the concentration of toxic elements in pheasant feathers was carried out by inductively coupled plasma mass spectrometry. The highest concentrations of Cr and Zn were found in birds from the Lubartów Forest District (1.93 mg/kg and 120.63 mg/kg, respectively), As and Ni in the Tomaszów Forest District (0.55 mg/kg and 1.60 mg/kg, respectively), Cd in the Lubartów Forest District and Skierniewice (0.04 mg/kg), and Pb in the Skierniewice Forest Distict (6.79 mg/kg). The observed results were strongly related to soil contamination and urbanization index, as key environmental factors which significantly determine the metal content in pheasant feathers. Therefore, proposed non-invasive measurements of the elemental composition of feathers of birds living in specific areas may be an important indicator of environmental pollution in relation to the high impact of anthropopressure.

Assessing the origin, genetic structure and demographic history of the common pheasant (Phasianus colchicus) in the introduced European range

The common pheasant, a game species widely introduced throughout the world, can be considered as an ideal model to study the effects of introduction events on local adaptations, biogeographic patterns, and genetic divergence processes. We aimed to assess the origin, spatial patterns of genetic variation, and demographic history of the introduced populations in the contact zone of Central and Southeast Europe, using mitochondrial DNA control region sequences and microsatellite loci. Both types of molecular markers indicated relatively low to moderate levels of genetic variation. The mtDNA analyses revealed that common pheasants across the study area are divided into two distinct clades: B (mongolicus group) and F (colchicus group). Analyses of the microsatellite data consistently suggested a differentiation between Hungary and Serbia, with the pheasant population in Hungary being much more genetically homogeneous, while that of Serbia has much more genetic mixture and admixture. This cryptic differentiation was not detected using a non-spatial Bayesian clustering model. The analyses also provided strong evidence for a recent population expansion. This fundamental information is essential for adequate and effective conservation management of populations of a game species of great economic and ecological importance in the studied geographical region.