The History of African Village Chickens: an Archaeological and Molecular Perspective

Chicken metabolism, immobilization, and post-industrial production

Chickens have become emblematic of the Anthropocene: They embody the age of acceleration, (post-) industrial value, and intensification in scientific and technological knowledge and practice. Contemporary chickens are the bearers of significant genetic and nutritional knowledge, experimented upon and 'tweaked' so much so that some have denied that contemporary commercial chickens are chickens at all. This article reconsiders chickens through a metabolic lens, and the notion of metabolism through chickens, arguing that attending to chickens opens up new conceptualizations of life and labour in the metabosphere. The article tells a metabolic history of chickens from ornament to enclosed monocrop, by way of the laboratory and nutritional experiments. Then, it looks at chicken metabolism in three conceptual modes: first, as a conduit for value, metabolizing and enhancing human life for the past century; second, through technological innovations extending the gut outside chickens' immobilized bodies; and third, through the planetary impacts of metabolic porosity in geological manifestations, toxic atmospheres, and viral overflow. Ultimately, this article shows how techno-scientific production of chickens has taken place in and created the metabosphere as a site of experimentation and exploitation.

Zooarchaeology of Managed, Captive, Tame, and Domestic Birds: Shifts in Human-Avian Relationships

In this paper, I review archaeological evidence for shifting human-avian interactions. Many species of birds, altering their behavior in response to anthropogenic niche construction, experienced an increased encounter rate with humans. Intensification of this relationship led to management and domestication of some taxa. An examination of the methods zooarchaeologists employ to study this changing interaction illustrates the limitations of evidence. Art history, architecture, historical sources, evidence based on modern distributions, and DNA analysis fill in some gaps in our knowledge. It is necessary to develop novel methods to investigate the earlier history of bird-human interactions. We also need to consider other taxa behaviorally amenable to domestication, as there was probably a diverse array of past human-bird relationships that remain unknown. Archaeologically, the relationship between people and birds is fundamental to understanding many symbolic and economic practices central to human societies. This review highlights the varied relationships between humans and birds globally allowing cross-regional examination.

The origin of genetic diversity of indigenous cockfighting chickens of Pakistan by analyzing the mtDNA

In Pakistan, the origin of the indigenous cockfighting chicken (ICC) or gamecock population is unknown. However, it is speculated that this might have been associated with domestication, an event linked to recreational, entertainment (cockfighting), religious or ornamental activities. This study aims to understand the origin and genetic diversity of the ICC population in Pakistan. A total of 185 ICC population and 10 captive Indian red junglefowl (Gallus gallus murghi) were analyzed for genetic diversity indices and phylogenetic reconstruction using a 397 bp of mtDNA D-loop region. It is reported that a total of 43 haplotypes from 38 polymorphic nucleotide sites. The haplotype and nucleotide diversity are also estimated in the range of 0.643-0.909, and 0.00585-0.01575, respectively. The total genetic diversity within the population was 91.52%. Four mitochondrial haplogroups A, B, C and D were identified by median-joining network analysis, two of them have high percentages, haplogroup D (81.6%) and A (15.1%). Phylogenetic analysis showed that the ICC population of Pakistan and Gallus gallus murghi shared haplogroup D. The results of this study showed that sub-haplogroup D17a05, has significantly high haplotype diversity and percentage as compared to previously published studies, this indicated that Pakistan might be one of the centres of domestication for chicken, as it is considered that Southeast Asia is the centre of domestication. Frequencies of Haplogroup A also indicate South-North indices. This research work showed that the indigenous cockfighting chicken population of Pakistan is genetically introgressed from Gallus gallus murghi, and significant variations could be attributed to the underlying differences in the geographics, selection pressures, introgression, and regional practices; and multiple origins of cockfighting chickens' populations around the world which reflected the past trading routes between human communities and civilizations.

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data

Introduction

The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale.

Methods

In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context.

Results and discussion

We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.

Origin and spatial population structure of Malagasy native chickens based on mitochondrial DNA

Since Malagasy human culture became established in a multi-layered way by genetic admixture of Austronesian (Indonesia), Bantu (East Africa) and West Asian populations, the Malagasy native livestock should also have originated from these regions. While recent genetic studies revealed that Malagasy native dogs and goats were propagated from Africa, the origin of Malagasy native chickens is still controversial. Here, we conducted a phylogeographic analysis of the native chickens, focusing on the historical relationships among the Indian Ocean rim countries and based on mitochondrial D-loop sequences. Although previous work suggested that the rare Haplogroup D occurs with high frequencies in Island Southeast Asia-Pacific, East Africa and Madagascar, the major mitochondrial lineage in Malagasy populations is actually not Haplogroup D but the Sub-haplogroup C2, which is also observed in East Africa, North Africa, India and West Asia. We demonstrate that the Malagasy native chickens were propagated directly from West Asia (including India and North Africa), and not via East Africa. Furthermore, they display clear genetic differentiation within Madagascar, separated into the Highland and Lowland regions as seen in the human genomic landscape on this island. Our findings provide new insights for better understanding the intercommunion of material/non-material cultures within and around Madagascar.

Temporal variation and risk factors associated with reproductive disorders in Hardhenu (Bos taurus × Bos indicus) dairy cattle

This study aimed to investigate the incidence and effect of non-genetic factors on reproductive disorders in the Hardhenu cattle population over a period of 11 years (2010-2021). The study included a total of 1340 cattle for calculating the incidence of reproductive disorders and analysed the occurrence of different reproductive disorders. In the present study, retention of placenta had highest frequency, accounting for approximately 18.36% of the incidence, followed by repeater cows (11.19%), metritis (6.27%), dystocia (0.60%), anestrus (0.45%) and prolapse (0.37%). Chi-square analysis revealed a significant relationship between the year and the incidence of reproductive disorders (p < .05). Logistic regression analysis of temporal variability of reproductive disorders was also analysed, with an increase in the odds from 2014 to 2020, peaking in 2017-2018 and 2018-2019. Logistic regression analysis showed that season and parity did not significantly influence the incidence of reproductive disorders. However, period of calving had a significant impact. Cows calving between 2008 and 2014 had a significantly lower odds ratio (0.13, 95% CI: 0.06-0.30), indicating a decreased risk, while those calving between 2014 and 2017 had a higher odds ratio (0.59, 95% CI: 0.38-0.90), suggesting an increased risk of reproductive disorders. Compared to parity 3, parity 1 (1.344, 95% CI: 0.869-2.08) and parity 2 (1.193, 95% CI: 0.768-1.851) showed highest odds ratio. Similarly, the odds ratio for winter (1.64, 95% CI: 0.93-2.89), summer (1.71, 95% CI: 0.89-3.26) and rainy season (1.64, 95% CI: 0.92-2.91) was higher as compared to autumn. The present results provided valuable insights into the incidence of various reproductive disorders and associated risk factors in Hardhenu cattle. These results can be utilized for targeted interventions to enhance reproductive health and overall productivity in dairy cattle.

Whole genome sequences of 234 indigenous African chickens from Ethiopia

Indigenous chickens predominate poultry production in Africa. Although preferred for backyard farming because of their adaptability to harsh tropical environments, these populations suffer from relatively low productivity compared to commercial lines. Genome analyses can unravel the genetic potential of improvement of these birds for both production and resilience traits for the benefit of African poultry farming systems. Here we report whole-genome sequences of 234 indigenous chickens from 24 Ethiopian populations distributed under diverse agro-climatic conditions. The data represents over eight terabytes of paired-end sequences from the Ilumina HiSeqX platform with an average coverage of about 57X. Almost 99% of the sequence reads could be mapped against the chicken reference genome (GRCg6a), confirming the high quality of the data. Variant calling detected around 15 million SNPs, of which about 86% are known variants (i.e., present in public databases), providing further confidence on the data quality. The dataset provides an excellent resource for investigating genetic diversity and local environmental adaptations with important implications for breed improvement and conservation purposes.

Measurement(s)	genome
Technology Type(s)	DNA sequencing
Factor Type(s)	animal population
Sample Characteristic - Organism	Gallus gallus
Sample Characteristic - Location	Ethiopia

Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.16999891

Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens

Breeding for climate resilience is currently an important goal for sustainable livestock production. Local adaptations exhibited by indigenous livestock allow investigating the genetic control of this resilience. Ecological niche modeling (ENM) provides a powerful avenue to identify the main environmental drivers of selection. Here, we applied an integrative approach combining ENM with genome-wide selection signature analyses (XPEHH and Fst) and genotype-environment association (redundancy analysis), with the aim of identifying the genomic signatures of adaptation in African village chickens. By dissecting 34 agro-climatic variables from the ecosystems of 25 Ethiopian village chicken populations, ENM identified six key drivers of environmental challenges: One temperature variable-strongly correlated with elevation, three precipitation variables as proxies for water availability, and two soil/land cover variables as proxies of food availability for foraging chickens. Genome analyses based on whole-genome sequencing (n = 245), identified a few strongly supported genomic regions under selection for environmental challenges related to altitude, temperature, water scarcity, and food availability. These regions harbor several gene clusters including regulatory genes, suggesting a predominantly oligogenic control of environmental adaptation. Few candidate genes detected in relation to heat-stress, indicates likely epigenetic regulation of thermo-tolerance for a domestic species originating from a tropical Asian wild ancestor. These results provide possible explanations for the rapid past adaptation of chickens to diverse African agro-ecologies, while also representing new landmarks for sustainable breeding improvement for climate resilience. We show that the pre-identification of key environmental drivers, followed by genomic investigation, provides a powerful new approach for elucidating adaptation in domestic animals.

Domestic chicken diversity: Origin, distribution, and adaptation

Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.

Investigating genetic diversity and population phylogeny of five Chongqing local chicken populations autosomal using microsatellites

The genetic diversity and population structures of five Chongqing local chicken populations were investigated using by 24 microsatellite markers. Results revealed that the mean number of alleles (N_A) ranged from 7.08 (Daninghe chicken, DN) to 8.46 (Nanchuan chicken, NC). The highest observed heterozygosity (H_O) and expected heterozygosity (H_E) were observed in DN (H_O = 0.7252; H_E = 0.7409) and the lowest H_O and H_E were observed in XS (Xiushan native chicken [XS], H_O = 0.5910 and H_E = 0.6697). The inbreeding coefficient (F_IS) within population ranged from 0.022 (DN) to 0.119 (XS). Among the 24 microsatellite markers, four loci (MCW0111, MCW0016, ADL0278, and MCW0104) deviated from the Hardy-Weinberg equilibrium in all the studied populations. The results of population polygenetic analysis based on Nei's genetic distance and STRUCTURE software showed that the clustering of the five populations was incomplete consistent with geographical distribution. Moreover, a large number of gene flows were widespread among different populations, suggesting that genetic material exchanges occurred due to human activities and migration which was also verified by PCoA. In summary, this study preliminarily showed that Chongqing local chicken populations had rich genetic diversity and remarkable genetic divergence, but still high risk in conversion. These findings would be useful to the management of conservation strategies and the utilization of local chicken populations in further.

Using phenotypic distribution models to predict livestock performance

Livestock production systems of the developing world use indigenous breeds that locally adapted to specific agro-ecologies. Introducing commercial breeds usually results in lower productivity than expected, as a result of unfavourable genotype by environment interaction. It is difficult to predict of how these commercial breeds will perform in different conditions encountered in e.g. sub-Saharan Africa. Here, we present a novel methodology to model performance, by using growth data from different chicken breeds that were tested in Ethiopia. The suitability of these commercial breeds was tested by predicting the response of body weight as a function of the environment across Ethiopia. Phenotype distribution models were built using machine learning algorithms to make predictions of weight in the local environmental conditions based on the productivity for the breed. Based on the predicted body weight, breeds were assigned as being most suitable in a given agro-ecology or region. We identified the most important environmental variables that explained the variation in body weight across agro-ecologies for each of the breeds. Our results highlight the importance of acknowledging the role of environment in predicting productivity in scavenging chicken production systems. The use of phenotype distribution models in livestock breeding is recommended to develop breeds that will better fit in their intended production environment.

Phenotypic and morphometric differentiation of indigenous chickens from Kenya and other tropical countries augments perspectives for genetic resource improvement and conservation

Indigenous chickens at the Swahili coast and other traditional migratory corridors in Kenya represent important populations that are inconclusively characterized. Using a comprehensive dataset of Kenyan indigenous chickens and additional mined data of chickens from 8 African and 5 Asian countries, we performed univariate and multivariate assessments to uncover the underlying phenotypic and morphometric variability. Kenyan indigenous chickens expressed differentiation of several qualitative and quantitative traits, both among different counties in the Swahili coast, and among coastal, western, and northern migratory corridors. There was a substantial population stratification of these chickens, particularly distinctive clustering of chickens from Marsabit, Lamu, and Kilifi counties. The pooled dataset further clarified a closer phenotypic and morphometric proximity of chickens within different geographical regions. We additionally revealed a preponderance of bantam and rumpless traits to hot and humid locales, and feathered shanks to cooler regions. Currently, most chicken breeding programs in developing countries rely on phenotypic and morphometric properties. Hence, the high chicken diversity and population stratification observed in our study, possibly shaped by natural and artificial selective pressures, reveal opportunities for complementary phenotypic and genotypic assessments to identify resources for effective breed improvement and conservation strategies of indigenous chickens in the tropics.

Genetic diversity of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania based on Major Histocompatibility Complex-linked microsatellite LEI0258 marker typing

Unraveling the genetic diversity of livestock species is central to understanding their value and importance for conservation and improvement in diverse production environments. In developing countries, information on genetic attributes of many livestock species is unfortunately scanty to support well-informed decision-making upon relevant management strategies. This study aimed at investigating allelic variability, genetic diversity, and genetic relationships of 10 indigenous chicken ecotypes from Southern Highlands of Tanzania using the Major Histocompatibility Complex-linked LEI0258 marker. A total of 400 DNA samples, 40 per ecotype, were genotyped by capillary electrophoresis. Thirty different alleles with sizes ranging from 197 to 569 bp were determined. The number of alleles ranged from 17 (Itunduma) to 21 (Mbeya), with an average of 19.20 alleles per ecotype. Allelic polymorphism was further evaluated through genotyping by Sanger sequencing. Thirty-three DNA samples with different fragment sizes were re-amplified and their alleles sequenced to depict polymorphism based on a combination of two repeat regions at 12 and 13 bp, respectively, and flanking regions with SNP and indels. The repeat region at 13 bp appeared 1 to 28 times, whereas the region at 12 bp appeared 3 to 19 times in all sequenced fragments. The numbers of indels and SNP determined were 7 and 9, respectively. From capillary electrophoresis, the Chunya and Msimbazi ecotypes exhibited the highest genetic diversity (0.937), whereas the lowest value (0.910) was observed from the Mbarali ecotype, with an average of 0.925. The Namtumbo and Wanging'ombe ecotypes showed high inbreeding coefficients (FIS > 0.05), whereas a high excess heterozygote value (FIS = -0.098) was observed from the Njombe ecotype. Two percent of the genetic diversity was due to differences among ecotypes, and the rest was due to differences among individuals within the ecotypes. Despite the overall low genetic differentiation, both fragment and sequencing analyses depicted a high allelic and genetic variability across 10 chicken ecotypes. These results therefore, underscore the importance of establishing appropriate conservation and management strategies to capitalize on observed variability and maintain genetic flexibility across diverse production environments.

The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution

BACKGROUND

Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been formed and those represent the diversity of the species. However, other than the natural evolutionary forces, management practices (including those that threaten the persistence of genetic diversity) following domestication have shaped the genetic make-up of and diversity between today's chicken breeds. As part of the SYNBREED project, samples from a wide variety of chicken populations have been collected across the globe and were genotyped with a high density SNP array. The panel consists of the wild type, commercial layers and broilers, indigenous village/local type and fancy chicken breeds. The SYNBREED chicken diversity panel (SCDP) is made available to serve as a public basis to study the genetic structure of chicken diversity. In the current study we analyzed the genetic diversity between and within the populations in the SCDP, which is important for making informed decisions for effective management of farm animal genetic resources.

RESULTS

Many of the fancy breeds cover a wide spectrum and clustered with other breeds of similar supposed origin as shown by the phylogenetic tree and principal component analysis. However, the fancy breeds as well as the highly selected commercial layer lines have reduced genetic diversity within the population, with the average observed heterozygosity estimates lower than 0.205 across their breeds' categories and the average proportion of polymorphic loci lower than 0.680. We show that there is still a lot of genetic diversity preserved within the wild and less selected African, South American and some local Asian and European breeds with the average observed heterozygosity greater than 0.225 and the average proportion of polymorphic loci larger than 0.720 within their breeds' categories.

CONCLUSIONS

It is important that such highly diverse breeds are maintained for the sustainability and flexibility of future chicken breeding. This diversity panel provides opportunities for exploitation for further chicken molecular genetic studies. With the possibility to further expand, it constitutes a very useful community resource for chicken genetic diversity research.

The broiler chicken as a signal of a human reconfigured biosphere

Changing patterns of human resource use and food consumption have profoundly impacted the Earth's biosphere. Until now, no individual taxa have been suggested as distinct and characteristic new morphospecies representing this change. Here we show that the domestic broiler chicken is one such potential marker. Human-directed changes in breeding, diet and farming practices demonstrate at least a doubling in body size from the late medieval period to the present in domesticated chickens, and an up to fivefold increase in body mass since the mid-twentieth century. Moreover, the skeletal morphology, pathology, bone geochemistry and genetics of modern broilers are demonstrably different to those of their ancestors. Physical and numerical changes to chickens in the second half of the twentieth century, i.e. during the putative Anthropocene Epoch, have been the most dramatic, with large increases in individual bird growth rate and population sizes. Broiler chickens, now unable to survive without human intervention, have a combined mass exceeding that of all other birds on Earth; this novel morphotype symbolizes the unprecedented human reconfiguration of the Earth's biosphere.

Use of geographic information system tools to predict animal breed suitability for different agro-ecological zones

Predicting breed-specific environmental suitability has been problematic in livestock production. Native breeds have low productivity but are thought to be more robust to perform under local conditions than exotic breeds. Attempts to introduce genetically improved exotic breeds are generally unsuccessful, mainly due to the antagonistic environmental conditions. Knowledge of the environmental conditions that are shaping the breed would be needed to determine its suitability to different locations. Here, we present a methodology to predict the suitability of breeds for different agro-ecological zones using Geographic Information Systems tools and predictive habitat distribution models. This methodology was tested on the current distribution of two introduced chicken breeds in Ethiopia: the Koekoek, originally from South Africa, and the Fayoumi, originally from Egypt. Cross-validation results show this methodology to be effective in predicting breed suitability for specific environmental conditions. Furthermore, the model predicts suitable areas of the country where the breeds could be introduced. The specific climatic parameters that explained the potential distribution of each of the breeds were similar to the environment from which the breeds originated. This novel methodology finds application in livestock programs, allowing for a more informed decision when designing breeding programs and introduction programs, and increases our understanding of the role of the environment in livestock productivity.

Genomic Comparison of Indigenous African and Northern European Chickens Reveals Putative Mechanisms of Stress Tolerance Related to Environmental Selection Pressure

Global climate change is increasing the magnitude of environmental stressors, such as temperature, pathogens, and drought, that limit the survivability and sustainability of livestock production. Poultry production and its expansion is dependent upon robust animals that are able to cope with stressors in multiple environments. Understanding the genetic strategies that indigenous, noncommercial breeds have evolved to survive in their environment could help to elucidate molecular mechanisms underlying biological traits of environmental adaptation. We examined poultry from diverse breeds and climates of Africa and Northern Europe for selection signatures that have allowed them to adapt to their indigenous environments. Selection signatures were studied using a combination of population genomic methods that employed FST , integrated haplotype score (iHS), and runs of homozygosity (ROH) procedures. All the analyses indicated differences in environment as a driver of selective pressure in both groups of populations. The analyses revealed unique differences in the genomic regions under selection pressure from the environment for each population. The African chickens showed stronger selection toward stress signaling and angiogenesis, while the Northern European chickens showed more selection pressure toward processes related to energy homeostasis. The results suggest that chromosomes 2 and 27 are the most diverged between populations and the most selected upon within the African (chromosome 27) and Northern European (chromosome 2) birds. Examination of the divergent populations has provided new insight into genes under possible selection related to tolerance of a population's indigenous environment that may be baselines for examining the genomic contribution to tolerance adaptions.

Deeper insight into maternal genetic assessments and demographic history for Egyptian indigenous chicken populations using mtDNA analysis

This study principally sought to reveal the demographic expansion of Egyptian indigenous chickens (EIC) using representative breeds: Sinai (North), Fayoumi (Middle) and Dandarawi (South) of Egypt as well as to deeply clarify their genetic diversity, possible matrilineal origin and dispersal routes. A total of 33 partial mitochondrial DNA sequences were generated from EIC and compared with a worldwide reference dataset of 1290 wild and domestic chicken sequences. Study populations had 12 polymorphic variable sites and 7 haplotypes. A lack of maternal substructure between EIC was detected (F ST  = 0.003). The unimodal mismatch distribution and negative values of Tajima's D (-0.659) and Fu's Fs (-0.157) indicated demographic expansion among EIC and pointed to Fayoumi as the oldest EIC population. Egyptian haplotypes were clustered phylogenetically into two divergent clades. Their phylogeography revealed an ancient single maternal lineage of Egyptian chickens likely derived from Indian-Subcontinent. Moreover, a recent maternal commercial heritage possibly originated in Yunnan-Province and/or surrounding areas was admixed restrictedly into Sinai. It is implied that Egypt was an entry point for Indian chicken into Africa and its further dispersal route to Europe. This study provides a clue supporting the previous assumption that urged utilizing consistent founder populations having closely related progenitors for synthetizing a stabilized homogenous crossbreed as a sustainable discipline in breeding program.

In vivo anthelmintic efficacy of Aloe ferox, Agave sisalana, and Gunnera perpensa in village chickens naturally infected with Heterakis gallinarum

The study was conducted to determine the anthelmintic efficacy of Aloe ferox, Agave sisalana, and Gunnera perpensa against Heterakis gallinarum in village chickens. The chickens naturally infected with H. gallinarum were randomly divided into 14 groups of eight chickens and orally administered distilled water (negative control), mebendazole (positive control), and graded levels (50-, 100-, 200-, and 400-mg/kg doses) of the three plant extracts. At days 0, 7, and 14, the floatation technique was used to determine fecal egg counts and H. gallinarum worms from chicken ceca were counted at days 0 and 14. Egg count reduction percentage (ECR%) was high at day 7 for all the test materials except for A. sisalana (100 mg/kg) that had 33%. At day 14, ECR% was high for all the other test materials save for A. ferox (200 mg/kg), mebendazole, and distilled water which was 50, 32, and 50%, respectively. A. ferox (200 mg/kg), G. perpensa (200 and 400 mg/kg), and A. sisalana (50 and 100 mg/kg) had the highest (85, 78, 74, 86, and 73%, respectively) worm count reduction percentage. The plants had anthelmintic properties. Advocacy and utilization of these plants in improving the health of village chickens could lead to increased productivity, boosting profits for the poultry industry thereby enabling it to meet the supply of animal protein and enhance livelihoods. It is imperative to determine compounds in the crude extracts of these medicinal plants which are responsible for the anthelmintic activities and their mechanism of action.

Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long-range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa.