The chicken (Gallus gallus), like most avian species, has a very distinct karyotype consisting of many micro- and a few macrochromosomes. While it is known that recombination frequencies are much higher for micro- as compared to macrochromosomes, there is limited information on differences in linkage disequilibrium (LD) and haplotype diversity between these two classes of chromosomes. In this study, LD and haplotype diversity were systematically characterized in 371 birds from eight chicken populations (commercial lines, fancy breeds, and red jungle fowl) across macro- and microchromosomes. To this end we sampled four regions of ~1 cM each on macrochromosomes (GGA1 and GGA2), and four 1.5 -2 cM regions on microchromosomes (GGA26 and GGA27) at a high density of 1 SNP every 2 kb (total of 889 SNPs).

Background: The comparative analysis of genome sequences emerging for several avian species with the fully sequenced chicken genome enables the genome-wide investigation of selective processes in functionally important chicken genes. In particular, because of pathogenic challenges it is expected that genes involved in the chicken immune system are subject to particularly strong adaptive pressure. Signatures of selection detected by inter-species comparison may then be investigated at the population level in global chicken populations to highlight potentially relevant functional polymorphisms. Results: Comparative evolutionary analysis of chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genes identified interleukin 4 receptor alpha-chain (IL-4Rα), a key cytokine receptor as a candidate with a significant excess of substitutions at nonsynonymous sites, suggestive of adaptive evolution. Resequencing and detailed population genetic analysis of this gene in diverse village chickens from Asia and Africa, commercial broilers, and in outgroup species red jungle fowl (JF), grey JF, Ceylon JF, green JF, grey francolin and bamboo partridge, suggested elevated and balanced diversity across all populations at this gene, acting to preserve different high-frequency alleles at two nonsynonymous sites. Conclusion: Haplotype networks indicate that red JF is the primary contributor of diversity at chicken IL-4Rα: the signature of variation observed here may be due to the effects of domestication, admixture and introgression, which produce high diversity. However, this gene is a key cytokine-binding receptor in the immune system, so balancing selection related to the host response to pathogens cannot be excluded.

This study assessed the climate resilience and characterized the existing farming systems in steep terrain in the hilly regions in South Asia. The farming systems considered were at an elevation ≥300 m in the mountain regions of two sites from Sri Lanka (Hatton and Welimada) and one site each from Bangladesh (Chittagong) and Nepal (Jhikhu Khola). A Climate Resilience Index (CRIi) score, varying from 0 (negligible resilience) and 1 (very high resilience), was calculated for each household using 31 parameters under Adaptive Capacity (ADC), Absorptive Capacity (ABC) and Transformative Capacity (TC). To spatially represent the CRIi, the four study locations were mapped using Inverse Distance Weighted (IDW) interpolation technique of GIS. All 424 households in the study sites scored a CRIi between 0.36 and 0.76, while the average CRI was the highest in Hatton (0.67), followed by Welimada (0.60), Jhikhu Khola (0.59) and Chittagong (0.48). Different demographic, socioeconomic and environmental parameters have contributed to the level of climate resilience of farming system units. Identification of good management practices of the climate-resilient farming systems and implementing those practices in vulnerable systems would increase the resilience and well-being of farming communities in steep terrain of mountain regions in South Asia.

Several millennia of human-mediated translocation of non-native pig species (genus Sus ) to the islands of Wallacea and Oceania have considerably altered local ecosystems. To investigate the timing and trajectory of these introductions, we conducted both genomic analyses of 576 pig nuclear genomes and a geometric morphometric analysis of 708 modern and ancient dental remains. Our analyses demonstrate that free-living and domestic pigs in Wallacea and Oceania have diverse ancestries resulting from the introduction of multiple sequential pig populations followed by gene flow. Despite the variability in their genomic ancestry, these pigs all have a distinct tooth morphology as well as a genetic link to the Chinese domestic pig populations that accompanied the dispersal of Austronesian language speakers ~4000 to 3000 years ago via Taiwan and the Philippines.