Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation

Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway

Ten Simple Rules for Organizing a Virtual Conference—Anywhere

1 International Institute of Tropical Agriculture, Nairobi, Kenya, 2 Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom, 3 Department of Computer and Information Sciences, Covenant University, Ota, Nigeria, 4 Institute of Bioinformatics, Johannes Kepler University, Linz, Austria, 5 Moroccan Society for Bioinformatics Institute, Morocco, 6 South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa, 7 University of Cape Town, Cape Town, South Africa, 8 University of Notre Dame, South Bend, Indiana, United States of America, 9 Biotechnology Unit, University of Buea, Buea, South West Region, Cameroon, 10 International Livestock Research Institute, Nairobi, Kenya, 11 Biosciences Eastern and Central Africa, Nairobi, Kenya, 12 International Center of Insect Physiology and Ecology, Nairobi, Kenya, 13 Bioinformatics Organization, Hudson, Massachusetts, United States of America, 14 Bioinformatics Team, Center for Development of Advanced Computing, Pune University Campus, Pune, India, 15 Harvard School of Public Health, Boston, Massachusetts, United States of Americ

Third Report on Chicken Genes and Chromosomes 2015

Following on from the First Report on Chicken Genes and Chromosomes [Schmid et al., 2000] and the Second Report in 2005 [Schmid et al., 2005], we are pleased to publish this long-awaited Third Report on the latest developments in chicken genomics. The First Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released. This report comes at a time of huge technological advances (particularly in sequencing methodologies) which have allowed us to examine the chicken genome in detail not possible until now. This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015], with many more planned

[Avian cytogenetics goes functional] Third report on chicken genes and chromosomes 2015

High-density gridded libraries of large-insert clones using bacterial artificial chromosome (BAC) and other vectors are essential tools for genetic and genomic research in chicken and other avian species... Taken together, these studies demonstrate that applications of large-insert clones and BAC libraries derived from birds are, and will continue to be, effective tools to aid high-throughput and state-of-the-art genomic efforts and the important biological insight that arises from them

The effect of distance on maternal institutional delivery choice : Evidence from Malawi

In many low- and middle-income countries, geographical accessibility continues to be a barrier to health care utilization. In this paper, we aim to better understand the full relationship between distance to providers and utilization of maternal delivery services. We address three methodological challenges: non-linear effects between distance and utilization; unobserved heterogeneity through non-random distance “assignment”; and heterogeneous effects of distance. Linking Malawi Demographic Health Survey household data to Service Provision Assessment facility data, we consider distance as a continuous treatment variable, estimating a Dose-Response Function based on generalized propensity scores, allowing exploration of non-linearities in the effect of an increment in distance at different distance exposures. Using an instrumental variables approach, we examine the potential for unobserved differences between women residing at different distances to health facilities. Our results suggest distance significantly reduces the probability of having a facility delivery, with evidence of non-linearities in the effect. The negative relationship is shown to be particularly strong for women with poor health knowledge and lower socio-economic status, with important implications for equity. We also find evidence of potential unobserved confounding, suggesting that methods that ignore such confounding may underestimate the effect of distance on the utilization of health services

Diversity of genetic types of local chickens and introgression with commercial exotic strains in Cameroon

Local chicken in Cameroon has a great diversity that is not yet fully explored. The objective of this study was to evaluate the diversity in genetic types of local chickens in Cameroon and level of introgression with exotic strains on the basis of 25 microsatellite markers. The number of alleles per locus varied from 2 (MCW0103) to 22 (LEI0192), with an average of 9.04. The average Ne was 3.78, while the heterozygosity between loci ranged from 0.31 to 0.75 (Ho), 0.33 to 0.86 (He), 0.40 to 0.81 (UHe) and 0.37 to 0.77 (Ht) with means of 0.60; 0.69; 0.65 and 0.63 respectively for the observed, expected, unbiased and total heterozygosity. The inbreeding coefficients FIS, FIT and FST were 0.03, 0.12 and 0.09 respectively. Only an average 4/25 loci significantly deviates from the Hardy-Weinberg equilibrium. Among the local chicken types, the highest Ho was that of naked necks (0.66 ± 0.17). Feathered tarsus and naked necks have the highest diversity across loci (0.67 ± 0.33 and 0.67 ± 0.34). The commercial strains Hybro and Lohman Brown showed excessive inbreeding. Only 4% of the total molecular variance is attributable to phenotypic differences. The number of migrants was high (6.302) showing admixture among populations. The maximum Nei genetic distances are found between exotic broilers and layers strains. Genetic distances between commercial broilers strains and feathered tarsus and with the normal feathered chicken are moderately high but comparable. Genetic distances among types of local chicken are very low, and the genetic identities very high. The dendrograms reveals that genetic types of local chicken are at intermediate position between commercial broilers and layers. Within the cluster of Cameroon local chickens, it is noticed that the Frizzle local chicken is a much more distant sub-group from other four genetic types, while the feathered tarsus and normal feathered chicken are closer. Broilers and layers chicken are clearly divergent, unlike the genetic types of local chickens. Local chicken types have variable levels of introgression with the various exotic broilers and layers strains. The local normal feathered chicken, although differing from exotic strains presents various introgression levels ranging from low (Lohman Brown) to medium (Arbor Acres and Hybro) and high (Rhode Island Red). In general only 35% of the chicken genomes found in Cameroon could be considered as pure or fully belonging to their respective strains.Key words: chicken, diversity, genetic types, introgressio

Mx Is Dispensable for Interferon-Mediated Resistance of Chicken Cells against Influenza A Virus ▿

The type I interferon (IFN) system plays an important role in antiviral defense against influenza A viruses (FLUAV), which are natural chicken pathogens. Studies of mice identified the Mx1 protein as a key effector molecule of the IFN-induced antiviral state against FLUAV. Chicken Mx genes are highly polymorphic, and recent studies suggested that an Asn/Ser polymorphism at amino acid position 631 determines the antiviral activity of the chicken Mx protein. By employing chicken embryo fibroblasts with defined Mx-631 polymorphisms and retroviral vectors for the expression of Mx isoforms in chicken cells and embryonated eggs, we show here that neither the 631Asn nor the 631Ser variant of chicken Mx was able to confer antiviral protection against several lowly and highly pathogenic FLUAV strains. Using a short interfering RNA (siRNA)-mediated knockdown approach, we noted that the antiviral effect of type I IFN in chicken cells was not dependent on Mx, suggesting that some other IFN-induced factors must contribute to the inhibition of FLUAV in chicken cells. Finally, we found that both isoforms of chicken Mx protein appear to lack GTPase activity, which might explain the observed lack of antiviral activity

Third Report on Chicken Genes and Chromosomes 2015

Following on from the First Report on Chicken Genes and Chromosomes [Schmid et al., 2000] and the Second Report in 2005 [Schmid et al., 2005], we are pleased to publish this long-awaited Third Report on the latest developments in chicken genomics. The First Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released. This report comes at a time of huge technological advances (particularly in sequencing methodologies) which have allowed us to examine the chicken genome in detail not possible until now. This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015], with many more planned.This article is from Cytogenic and Genome Research 145 (2015): 78, doi:10.1159/000430927.</p