Species and Phenotypic Distribution Models Reveal Population Differentiation in Ethiopian Indigenous Chickens

Abstract

Smallholder poultry production dominated by indigenous chickens is an important source of livelihoods for most rural households in Ethiopia. The long history of domestication and the presence of diverse agroecologies in Ethiopia create unique opportunities to study the effect of environmental selective pressures. Species distribution models (SDMs) and Phenotypic distribution models (PDMs) can be applied to investigate the relationship between environmental variation and phenotypic differentiation in wild animals and domestic populations. In the present study we used SDMs and PDMs to detect environmental variables related with habitat suitability and phenotypic differentiation among nondescript Ethiopian indigenous chicken populations. 34 environmental variables (climatic, soil, and vegetation) and 19 quantitative traits were analyzed for 513 adult chickens from 26 populations. To have high variation in the dataset for phenotypic and ecological parameters, animals were sampled from four spatial gradients (each represented by six to seven populations), located in different climatic zones and geographies. Three different ecotypes are proposed based on correlation test between habitat suitability maps and phenotypic clustering of sample populations. These specific ecotypes show phenotypic differentiation, likely in response to environmental selective pressures. Nine environmental variables with the highest contribution to habitat suitability are identified. The relationship between quantitative traits and a few of the environmental variables associated with habitat suitability is non-linear. Our results highlight the benefits of integrating species and phenotypic distribution modeling approaches in characterization of livestock populations, delineation of suitable habitats for specific breeds, and understanding of the relationship between ecological variables and quantitative traits, and underlying evolutionary processes.

Ecological niche modelling for delineating livestock ecotypes and exploring environmental genomic adaptation: The example of Ethiopian village chicken

“…One of the limitations of our study is that we only used chicken populations that were available to us. Although the sampling was performed to represent major Ethiopian AEZs, no specific environmental-gradation approach was applied to inform the sampling, as has been done in a recent paper by Kebede et al (2021). Consequently, though fully valid, our study may not have surveyed all possible agro-climatic clines and the ecotypes presented here may not be an exhaustive list from Ethiopia.…”

“…As a consequence, the method has been a powerful tool in the conservation efforts of wild species (Thorn et al, 2009) and has found applications for other diverse purposes such as assessing the risk from invasive species (Jiménez-Valverde et al, 2011), epidemiological studies (Cardoso-Leite et al, 2014), and estimating the effect of climate change on future distribution of a species (Jeschke and Strayer, 2008). In livestock, however, the use of ENM is still in its infancy with only a few available examples (Pitt et al, 2016;Lozano-Jaramillo et al, 2018;Vajana et al, 2018;Gheyas et al, 2021;Kebede et al, 2021). Pitt et al (2016) used MaxEnt for inferring the actual and historical distributions of early domestic fowl by modelling the environmental conditions of extant Red Jungle Fowl (RJF) with important conservation implications.…”

“…In a recent study (Gheyas et al, 2021), we applied MaxEnt for identifying the key environmental drivers in the agro-ecologies of Ethiopian indigenous chickens, followed by genomic analyses in relation to these variables to identify candidate adaptive genes. In another recent study, Kebede et al (2021) integrated ENM with phenotypic distribution modelling to study phenotypic differentiation among Ethiopian indigenous chicken populations and used this characterisation for delineating potential ecotypes. The study, however, did not consider the genomic basis of adaptation.…”

Ecological niche modelling as a tool to identify candidate indigenous chicken ecotypes of Tigray (Ethiopia)

“…In livestock, the application of the ENM approach is still in its infancy, with only a few studies so far, primarily in chicken (Vajana et al, 2018;Lozano-Jaramillo et al, 2019;Gheyas et al, 2021;Kebede et al, 2021;Vallejo-Trujillo et al, 2022). Applying ENM on Ethiopian indigenous chickens, Gheyas et al (2021) identified six major environmental variables.…”

“…Then, the author chose the extreme environments to identify signatures of positive selection in the genome of these populations associated with the selected environmental parameters. Kebede et al (2021) studied Ethiopian environmental gradients and using ENM classified the indigenous Ethiopian chicken's habitats into three agro-ecologies. They reported significant morphological differences between the chicken populations among these agro-ecologies, supporting them as chicken ecotypes (Kebede et al, 2021).…”