The usefulness of maternally inherited genetic markers for phylogeographic studies in village chicken.

Phylogeography plays a major role in understanding micro and macroevolutionary processes dealing with evolutionary interpretations of geographical distribution. This field integrates information from molecular genetics, population genetics, demography, and phylogeny for the interpretation of the geographical distribution of lineages. The full mtDNA sequence and W chromosome polymorphisms were exploited to assess the usefulness of two maternally-inherited genetic markers for phylogeographic studies of village chickens. We studied 243 full mtDNA sequences from three countries (Iraq, n = 27; Ethiopia, n = 211; and Saudi Arabia, n = 5) and a 13-kb fragment of the W chromosome from 20 Iraqi and 137 Ethiopian female chickens. The results show a high level of genetic diversity for the mtDNA within and among countries as well as within populations. On the other hand, sequence analysis of the W chromosome shows low genetic diversity both within and among populations. Six full mtDNA haplogroups (A, B, C1, C2, D1, and E1) were observed and 25 distinct W haplotypes. The results support the effectiveness of full mtDNA sequences but not the W chromosome in tracing the maternal historical genome background with, however, weak within a country phylogeographic signal.

Natural adaptation and human selection of northeast African sheep genomes.

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ∼54× for 130 samples (Ethiopia, Libya) and ∼20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.

Maternal origin and genetic diversity of Algerian domestic chicken (Gallus gallus domesticus) from North-Western Africa based on mitochondrial DNA analysis.

Local chicken populations are a major source of food in the rural areas of Algeria. However, their origin has not been well characterized. The objectives of this study were to assess genetic diversity and maternal origin of domestic chicken from five agro-ecological regions of western Algeria: coastal (CT), inland plains (IP), highlands (HL), mountains (MT) and sahara (SH, including Oasis, Req and Erg regions). A set of 88 mitochondrial DNA (mtDNA) D-loop sequences including the hypervariable region I (HV1) were analyzed. From the 397 bp D-loop sequence, 20 variable sites that defined 13 haplotypes were identified in Algerian domestic chicken. The haplotype and nucleotide diversity were estimated as 0.597 and 0.003, respectively. Phylogenetic and network analyses indicated the presence of two clades or haplogroups (A and E). Only one clade A haplotype was observed exclusively in the population of mountains, while, Clade E haplotypes were found in almost all Algerian chicken with twelve different haplotypes. These findings suggest that Algerian chickens derived from the most ubiquitous haplogroup which have its root in the Indian subcontinent. Our results provide important information about the origin of the North-West African chicken and the historical dispersal of the first chicken populations into African continent.

Diversity of endogenous avian leukosis virus subgroup E (ALVE) insertions in indigenous chickens.

BACKGROUND: Avian leukosis virus subgroup E (ALVE) insertions are endogenous retroviruses (ERV) that are restricted to the domestic chicken and its wild progenitor. In commercial chickens, ALVE are known to have a detrimental effect on productivity and provide a source for recombination with exogenous retroviruses. The wider diversity of ALVE in non-commercial chickens and the role of these elements in ERV-derived immunity (EDI) are yet to be investigated. RESULTS: In total, 974 different ALVE were identified from 407 chickens sampled from village populations in Ethiopia, Iraq, and Nigeria, using the recently developed obsERVer bioinformatics identification pipeline. Eighty-eight percent of all identified ALVE were novel, bringing the known number of ALVE integrations to more than 1300 across all analysed chickens. ALVE content was highly lineage-specific and populations generally exhibited a large diversity of ALVE at low frequencies, which is typical for ERV involved in EDI. A significantly larger number of ALVE was found within or near coding regions than expected by chance, although a relative depletion of ALVE was observed within coding regions, which likely reflects selection against deleterious integrations. These effects were less pronounced than in previous analyses of chickens from commercial lines. CONCLUSIONS: Identification of more than 850 novel ALVE has trebled the known diversity of these retroviral elements. This work provides the basis for future studies to fully quantify the role of ALVE in immunity against exogenous ALV, and development of programmes to improve the productivity and welfare of chickens in developing economies.

The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa.

BACKGROUND: Indigenous domestic chicken represents a major source of protein for agricultural communities around the world. In the Middle East and Africa, they are adapted to hot dry and semi-dry areas, in contrast to their wild ancestor, the Red junglefowl, which lives in humid and sub-humid tropical areas. Indigenous populations are declining following increased demand for poultry meat and eggs, favouring the more productive exotic commercial breeds. In this paper, using the D-loop of mitochondrial DNA as a maternally inherited genetic marker, we address the question of the origin and dispersal routes of domestic chicken of the Middle East (Iraq and Saudi Arabia), the northern part of the African continent (Algeria and Libya) and the Horn of Africa (Ethiopia). RESULTS: The analysis of the mtDNA D-loop of 706 chicken samples from Iraq (n = 107), Saudi Arabia (n = 185), Algeria (n = 88), Libya (n = 23), Ethiopia (n = 211) and Pakistan (n = 92) show the presence of five haplogroups (A, B, C, D and E), suggesting more than one maternal origin for the studied populations. Haplogroup E, which occurred in 625 samples, was the most frequent in all countries. This haplogroup most likely originates from the Indian subcontinent and probably migrated following a terrestrial route to these different countries. Haplotypes belonging to haplogroup D were present in all countries except Algeria and Libya, it is likely a legacy of the Indian Ocean maritime trading network. Haplogroup A was present in all countries and may be of commercial origin. Haplogroup B was found only in Ethiopia. Haplogroup C was only detected in the South-Western region of Saudi Arabia and in Ethiopia. CONCLUSION: The results support a major influence of the Indian subcontinent on the maternal diversity of the today's chicken populations examined here. Most of the diversity occurs within rather than between populations. This lack of phylogeographic signal agrees with both ancient and more recent trading networks having shaped the modern-day diversity of indigenous chicken across populations and countries.