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Over the last decades, the study of the microbiome has been receiving increasing attention as a major driver of individual health and wellbeing. The accumulation of knowledge on microbiomes sparked new research lines, from which the association between oral microbiome composition and taste perception is of great interest. Taste plays a paramount role in food and beverage choice as well as emotions. For wine tasters, the smell is also part of the tasting evaluation. However, the nasal microbiome is relatively unexplored. The relation between the microorganisms residing in the nostrils is still poorly known despite their leading role in flavor perception. Therefore, characterizing the composition of nasal microbiomes represents a fundamental prerequisite to elucidate their relationship with taste. To improve our understanding of the relationship between taste and the microorganism inhabiting the nostrils, the nasal microbiome of 5 wine tasters versus 5 non-tasters was analyzed through the sequencing of the V3-V4 region of the16S rRNAgene. The taxonomic composition of these nasal microbiomes was characterized, and the comparison of diversity indexes revealed no significant differences. However, the experimental group showed a lower number of identified taxa (171) when compared to the control group (287). Another interesting result was the higher presence of Krebs Cycle pathways in wine tasters, which could indicate the importance of the nostril bacterial community in alcohol oxidation. Regarding smoking habits, smokers presented a lower microbiome diversity. These preliminary results should be confirmed in a larger sample dataset of wine tasters and controls.

Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa similar to 5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant similar to 200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military. French National Research Agency (ANR) ANR-10-INBS-09 info:eu-repo/semantics/publishedVersion

Taste plays a paramount role in food and beverage choice, with recent studies pointing to a potential influence of the microorganisms from the tongue dorsum - particularly bacteria - on flavor perception. Thus, the association between tongue dorsum biofilm and taste is a fundamental prerequisite for a better understanding of the role played by these bacteria in wine tasting. To study this impact, we have analyzed the microbiomes from 58 samples of the tongue dorsum surface from professional wine tasters and 30 samples from non professional wine tasters. The microbiome of each sample was characterized through metagenome sequencing of the 16S rRNA gene for taxonomic discrimination of bacteria. A total of 497 taxa were identified in the tongue dorsum, and significant differences in diversity were observed between the wine taster and the control group. The comparison of bacterial diversity between samples collected before and after wine tasting along with the presence of new bacterial taxa indicates a direct effect of wine on the microbiome of frequent wine tasters, particularly in those tasting sparkling wines.

This datasheet on Equus asinus covers Identity, Overview, Distribution, Dispersal, Biology & Ecology, Impacts, Uses, Prevention/Control, Further Information.

The present study examined a set of 10 microsatellites/minisatellites and analyzed the genetic structure ofA high level of genetic diversity was observed amongThe

Description, Hybridization footprint suggests introgression with local wild relatives in Western European grape varieties., Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties showing large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by gene flow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.

The genetic diversity of most global goat populations has been assessed in recent decades using nuclear markers but remains unstudied in the south Arabian Peninsula, particularly in the Sultanate of Oman, despite the importance of these animals for the local economy and food supply. Therefore, the present study provides a comparative analysis of the genetic diversity of five native Omani goat populations and evaluates possible admixture rates with the four most frequently imported goat populations from geographically proximal countries. A dataset based on 11 highly informative microsatellite locus genotypes from nine populations was used to estimate population genetic parameters. The summary statistics for the parameters depicted relatively highly diverse populations (Ho = 0.667, He = 0.663) with relatively low and mostly non-significant levels of inbreeding (FIS). Furthermore, population substructure estimators (AMOVA) and population differentiation coefficient (FST) indicated weak genetic differentiation among populations (P

Domestic chicken populations have been subjected to selection strategies to improve different production traits. Throughout history, selection coupled with diverse demographic dynamics have shaped the genome of many local populations which might harbor important genetic combinations with potential for production and survival to future unknown climate changes. South American local chickens include several well-adapted local breeds that thrive in extreme environments (e.g., tropical rain forest, high altitude and desert). In addition, there has been a long tradition of game fowl breeding in South America about which very little is known. As game fowl display distinct phenotypes compared to other types of chickens, i.e., aggressiveness, we have screened for single nucleotide polymorphisms (SNPs) localized in genes related to behavior that depart from neutrality (i.e., outliers) and therefore might be influenced by selection. Here we used restriction site-associated DNA sequencing (RADseq) to identify 122,801 SNPs distributed across the genome to scan for selection signatures in South American chicken populations. We detected 892 SNPs that were under selection. Two SNPs under positive selection localized in a genomic region harboring the Dopamine Receptor 2 (DRD2) gene and the Ankyrin Repeat and Kinase Domain Containing 1 (ANKK1) gene which have been associated with behavior. The population branch statistics analysis (PBS) on these two SNPs provided further evidence that these two variants have been under positive selection in game fowl. These findings contribute to the understanding of the genetic architecture behind the aggressiveness behavior in chickens, a trait of paramount importance in the poultry industry.

We investigated the genetic diversity and population genetic structure of six morphologically distinct Ethiopian donkey populations using 12 equine microsatellite markers. The donkey populations were Abyssinian (AB), Afar (AF), Hararghe (HA), Ogaden (OG), Omo (OM) and Sinnar (SI). Blood samples were collected from 180 genetically unrelated donkeys (30 individuals per population). Population genetic diversity estimates showed that total number and mean number of observed alleles, average observed and expected heterozygosity were 94, 5.208 ± 0.0229, 0.555 ± 0.023 and 0.588 ± 0.022, respectively. Highly significant deficiency in heterozygote was detected within the overall samples (FIS = 0.055 ± 0.021; P < 0.001). Though highly significant (P < 0.001), heterozygote deficiency within populations relative to total population was moderate (FST = 0.046 ± 0.016), suggesting a higher diversity within the populations (95.4%) than between populations. Various genetic distance estimation methods produced a similar topology of un-rooted dendrograms that grouped the overall Ethiopian donkeys into lowland (Ogaden, Omo and Sinnar) and highland (Abyssinian, Afar and Hararghe) genetic lineages. Likewise, Bayesian clustering analysis produced a similar pattern of clustering that was highly concordant with traditional donkey classification systems in Ethiopia.

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds&rsquo, linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size., Part of the research presented in this publication was funded by grant AGL2013–48742-C2–1-R awarded by the Spanish Ministry of Economy as well as by projects TKISSE and TGENRE supported by the Hungarian Ministry of Agriculture. The authors also acknowledge the support of the Spanish Ministry of Economy and Competitivity for the Center of Excellence Severo Ochoa 2016-2019 (SEV-2015-0533) grant awarded to the Centre for Research in Agricultural Genomics (CRAG). Tainã Figueiredo Cardoso was funded with a fellowship from the CAPES Foundation-Coordination of Improvement of Higher Education, Ministry of Education of the Federal Government of Brazil. Thanks also to the CERCA Programme of the Generalitat de Catalunya.

Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease that is becoming a significant global health care problem. Several studies have shown that people with diabetes are more susceptible to oral problems, such as periodontitis and, although the causes are still inconclusive, the oral microbiota seems to be an important factor in this interaction. This study aimed to characterize the oral microbiome of a sample representing T2DM patients from Portugal and exploit potential associations between some microorganisms and variables like teeth brushing, smoking habits, and nutrient intake. By sequencing the hypervariable regions V3-V4 of the 16S rRNA gene in 50 individuals belonging to a group of diabetes patients and a control group, we found a total of 233 taxa, from which only 65% were shared between both groups. No differences were found in terms of alpha and beta diversity between groups or habits categories. Also, there were no significant differences in the oral microbiome profiles of control and diabetes patients. Only the class Synergistia and the genus TG5, which are related to periodontitis, were statistically more frequent in the control group. This finding can be justified by the fact that these diabetic patients usually have their oral health under close medical control than an average healthy person, which in this study was represented by the control group.IMPORTANCEDiabetes has become a significant global health care issue as its incidence continues to increase exponentially, with type 2 diabetes being responsible for more than 90% of these cases. Portugal is one of the countries with a higher prevalence of diabetes in Europe. It has been reported that diabetic people have an increased risk of developing several health problems such as oral infections mostly caused by opportunistic pathogens. Some studies have pointed out a relationship between diabetes and oral microbiome. Therefore, the characterization of the microbial ecosystem of the mouth in reference groups is crucial to provide information to tackle oral health pathogen-borne conditions. In this study, we provide the first characterization of the oral microbiome of type 2 diabetes mellitus patients from Portugal, and therefore, contributing new data and knowledge to elucidate the relationship between diabetes and the oral microbiome.

All tropically adapted humped cattle (Bos indicus or “zebu”), descend from a domestication process that took place >8,000 years ago in South Asia. Here we present an intercontinental survey of Y-chromosome diversity and a comprehensive reconstruction of male-lineage zebu cattle history and diversity patterns. Phylogenetic analysis revealed that all the zebu Y-chromosome haplotypes in our dataset group within three different lineages: Y3A, the most predominant and cosmopolitan lineage; Y3B, only observed in West Africa; and Y3C, predominant in South and Northeast India. The divergence times estimated for these three Zebu-specific lineages predate domestication. Coalescent demographic models support either de novo domestication of genetically divergent paternal lineages or more complex process including gene flow between wild and domestic animals. Our data suggest export of varied zebu lineages from domestication centres through time. The almost exclusive presence of Y3A haplotypes in East Africa is consistent with recent cattle restocking in this area. The cryptic presence of Y3B haplotypes in West Africa, found nowhere else, suggests that these haplotypes might represent the oldest zebu lineage introduced to Africa ca. 3,000 B.P. and subsequently replaced in most of the world. The informative ability of Interspersed Multilocus Microsatellites and Y-specific microsatellites to identify genetic structuring in cattle populations is confirmed.

The ability to adapt to harsh environments and thrive with minimal food and water input, places goats among the most popular livestock species in Arab countries. However, little is known about the historical and contemporary genetics of most Arabian goat breeds and populations. In this study, we genetically analyzed 617 individuals (126 from this study and 491 from published sources) representing 18 Arabian goat populations by evaluating variation in the mitochondrial DNA control region (D-loop). Our data were also combined and compared with those from 339 Asian, African, European and Canarian populations. We found 186 different polymorphic sites, which allowed us to identify 453 different haplotypes belonging to three maternal haplogroups: A, B and G. Haplogroup A is the most represented among Arabian goats and highly widespread among Arab countries, whereas B group is rare. Haplogroup G is the second most frequent haplogroup and also the most diverse among Arabian goats. Measurements of nucleotide and haplotype diversity and the mean number of pairwise differences in the 18 populations yielded values of 0.025, 0.998 and 10.586, respectively. These results show that the diversity of native Arabian goat populations is high and similar to that of populations at the center of origin. Based on estimated population structures, comparison of pairwise F ST and AMOVA values between Arabian populations indicated low genetic differentiation. In addition, median-joining network analysis results provide very little evidence of a previous connection between Arabian goats and regions of historical Arab influence were once installed (Iberian Peninsula and Southern Europe). Finally, the same thin evidence was also found between extant Arabian and Canarian goats, which might have partially originated due to commercial trade or during the migratory movements of ancient humans.

A small population of Asiatic black bear—known as the Baluchistan black bear—survives in the western limit of the species’ range in Iran, where the species is rare, difficult to monitor and occupy an atypical habitat with extreme environmental conditions. Through the use of noninvasively collected samples, we analyzed mitochondrial DNA control region sequences to evaluate the phylogenetic relationships and divergence time between the Baluchistan Iranian black bear population and other Asian populations. Phylogenetic analyses indicate that Baluchistan and Nepalese (Himalayan) populations are monophyletic, with their divergence time estimated at circa 120 thousand years ago. The results reveal the low level of mitochondrial DNA variability in this small and marginal population, as is the case for many bear populations living in areas with similar conditions. The divergence time between the populations from Iran and Nepal dates to the Late Pleistocene, pointing to a transitional period between colder (glacial) and warmer (interglacial) conditions that allowed forests to expand and opened new habitats to population expansions. Pending further genetic and morphological corroboration, these preliminary results suggest that all Baluchistan and Himalayan (Nepalese) black bears might be considered as synonymous under the priorU. t. thibetanustrinomial (withgedrosianusjust as junior synonym). Conservation efforts on this small and endangered population remain poor, and further measures are required to guarantee its long-term survival in Iran.

The Apicomplexan parasites, Theileria lestoquardi and Theileria annulata, the causative agents of theileriosis in small and large ruminants, are widespread in Oman, in areas where cattle, sheep and goats co-graze. Genetic analysis can provide insight into the dynamics of the parasite and the evolutionary relationship between species. Here we identified ten genetic markers (micro- and mini-satellites) spread across the T. lestoquardi genome, and confirmed their species specificity. We then genotyped T. lestoquardi in different regions in Oman. The genetic structures of T. lestoquardi populations were then compared with previously published data, for comparable panels of markers, for sympatric T. annulata isolates. In addition, we examined two antigen genes in T. annulata (Tams1 and Ta9) and their orthologues in T. lestoquardi (Tlms1 and Tl9).\ud \ud The genetic diversity and multiplicity of infection (MOI) were lower in T. lestoquardi (He = 0.64–0.77) than T. annulata (He = 0.83–0.85) in all populations. Very limited genetic differentiation was found among T. lestoquardi and T. annulata populations. In contrast, limited but significant linkage disequilibrium was observed within regional populations of each species. We identified eight T. annulata isolates in small ruminants; the diversity and MOI were lower among ovine/caprine compared to bovine. Sequence diversity of the antigen genes, Tams1 and Ta9 in T. annulata (π = 0.0733 and π = 0.155 respectively), was 10-fold and 3-fold higher than the orthologous Tlms1 and Tl9 in T. lestoquardi (π = 0.006 and π = 0.055, respectively).\ud \ud Despite a comparably high prevalence, T. lestoquardi has lower genetic diversity compared to sympatric T. annulata populations. There was no evidence of differentiation among populations of either species. In comparison to T. lestoquardi, T. annulata has a larger effective population size. While genetic exchange and recombination occur in both parasite species, the extent of diversity, overall, is less for T. lestoquardi. It is, therefore, likely that T. lestoquardi evolved from an ancestor of present day T. annulata and that this occurred either once or on a limited number of occasions.

The extremely endangered Gochu Asturcelta pig breed was analysed to document its genetic background and to ascertain if the traditional classification of native pig of the Iberian Peninsula into the Celtic-Iberian and the Iberian groups has genetic support. Two populations of Gochu Asturcelta pig (initial and present, including 31 and 124 individuals, respectively) were typed for 17 microsatellites together with 137 individuals of four domestic pig populations (eight breeds) and Wild Boar. Gochu Asturcelta populations showed a noticeable genetic distance with the other populations analysed due to the extreme bottleneck suffered by the breed. In any case, differentiation between the two Gochu Asturcelta populations analysed was very low (F ST =0.021±0.005). Morever, the two Gochu Asturcelta populations took basically the same values (1.14 and 1.13, respectively) for parameter N g (founder genome equivalents) suggesting that the Gochu Asturcelta breed has not suffered additional genetic losses of genetic variability due to drift after the implementation of the breeding scheme. A total of 174 mtDNA control region fragments (647 bp) were analysed allowing the identification of 30 different haplotypes. Gochu Asturcelta had only three different haplotypes. The most frequent haplotypes H3 (18% of the samples; assigned to Larson et al.'s haplogropup A) and H5 (25% of the samples; assigned to Larson et al.'s haplogropup C) could be identified in all the Celtic-Iberian, Iberian and Cosmopolitan pig breeds analysed. This makes difficult to ensure that the classical hypothesis explaining different origins for the native pig strains of the Iberian Peninsula has genetic support. Projection of the mitochondrial DNA genetic variability (summarised via Principal Component Analysis) on geographical maps informed that the mtDNA composition of domestic pig native of the Iberian Peninsula depicts the recent rather than the ancient history of the analysed populations.

The spread of domestic animals through time is one of the topics studied by archaeologists to assess human trade and migration. Here we present mitochondrial analysis of 42 archaeological cattle ( Bos taurus ) bone samples, from 16 different sites in the Iberian Peninsula and covering a broad timeframe (from the early Neolithic to the Middle Ages), to provide evidence about the origin and dispersion of the T1 cattle haplogroup in relation to human contacts and movements. The presence of the T1 haplotype in one sample from an early Neolithic site close to the Mediterranean coast of Iberia, and its continuing presence in the Peninsula during Roman and Medieval times, clearly demonstrates that T1 was not solely a Muslim or later introduction. Rather, our molecular data show evidence for a pioneer coastal colonisation of the Iberian Peninsula from the Mediterranean basin, followed by possible further colonisation, leading to a continuity of diversity through time.

All extant equid species are grouped in a single genus – Equus. Among those, ass-like equids have remained particularly unstudied and their phylogenetic relations were poorly understood, most probably because they inhabit extreme environments in remote geographic areas. To gain further insights into the evolutionary history of ass-like equids, we have used a non-invasive sampling approach to collect representative fecal samples of extant African and Asiatic ass-like equid populations across their distribution range and mitochondrial DNA (mtDNA) sequencing analyses to examine intraspecific genetic diversity and population structure, and to reconstruct phylogenetic relations among wild ass species/subspecies. Sequence analyses of 410 base pairs of the fast evolving mtDNA control region identified the Asiatic wild ass population of Kalamaili (China) as the one displaying the highest diversity among all wild ass populations. Phylogenetic analyses of complete cytochrome b sequences revealed that African and Asiatic wild asses shared a common ancestor approximately 2.3 Mya and that diversification in both groups occurred much latter, probably driven by climatic events during the Pleistocene. Inferred genetic relationships among Asiatic wild ass species do not support E. kiang monophyly, highlighting the need of more extensive studies in order to clarify the taxonomic status of species/subspecies belonging to this branch of the Equus phylogeny. These results highlight the importance of re-assessing the evolutionary history of ass-like equid species, and urge to extend studies at the population level to efficiently design conservation and management actions for these threatened species.

Donkey domestication drastically changed ancient transport systems in Africa and Asia, enabling overland circulation of people and goods and influencing the organization of early cities and pastoral societies. Genetic studies based on mtDNA have pointed to the African wild ass as the most probable ancestor of the domestic donkey, but questions regarding its center of origin remain unanswered. Endeavoring to pinpoint the geographical origin of domestic donkey, we assessed levels and patterns of genetic diversity at 15 microsatellite loci from eight populations, representing its three hypothesized centers of origin: northeast Africa, the Near East and the Arabian Peninsula. Additionally, we compared the donkey genotypes with those from their wild relative, the African wild ass (Equus africanus somaliensis) to visualize patterns of differentiation among wild and domestic individuals. Obtained results revealed limited variation in levels of unbiased expected heterozygosity across populations in studied geographic regions (ranging from 0.637 in northeast Africa to 0.679 in the Near East). Both allelic richness (Ar) and private allelic richness presented considerably higher values in northeast Africa and in the Arabian Peninsula. By looking at variation at the country level, for each region, we were able to identify Sudan and Yemen as the countries possessing higher allelic richness and, cumulatively, Yemen also presented higher values for private allelic richness. Our results support previously proposed northeast Africa as a putative center of origin, but the high levels of unique diversity in Yemen opens the possibility of considering this region as yet another center of origin for this species.

Background In the Arabian Peninsula malaria control is progressing steadily, backed by adequate logistic and political support. As a result, transmission has been interrupted throughout the region, with exception of limited sites in Yemen and Saudi Arabia. Here we examined Plasmodium falciparum parasites in these sites to assess if the above success has limited diversity and gene flow. Methods We examined 108 P. falciparum isolates in three sites in Yemen (Taiz, Dhamar and Hodeidah) and 91 isolates from Saudi Arabia (Jazan). Nine microsatellites were analyzed for allelic diversity, multi-locus haplotype and inter-population differentiation. Results Diversity at each locus (unbiased heterozygosity [H]) was relatively lower in Yemen; (Hodeidah, H = 0.615, Taiz, H = 0.66, Dhamar, H = 0.481), compared to Saudi Arabia (Jazan, H = 0.76). Microsatellites were distributed widely and private alleles, detected in a single population, were rare. Pairwise comparisons revealed that parasites population in Dhamar was relatively distanced (FST = 0.19). However, Taiz (Yemen) (FST = 0.065) and Hodeidah (FST = 0.107) populations were closer to that in Jazan (Saudi Arabia). Nonetheless, parasites in the four sites can be considered as one population. Conclusion Although malaria risk in Saudi Arabia has been cut considerably, the extent of diversity and parasite genetic structure are indicative of a large population size. Elimination strategy should target demographic factors that favor parasite dispersal and flow of imported malaria.

We investigated mitochondrial DNA (mtDNA) sequence polymorphism of six morphologically diverse domestic donkey (Equus asinus) populations in Ethiopia. These populations include: Abyssinian (AB), Afar (AF), Hararghe (HR), Ogaden (OG), Omo (OM) and Sinnar (SI). Genetic relationships and other diversity parameters were inferred from 39 randomly selected mtDNA D-loop partial sequences, characterized by 29 polymorphic sites defining 19 distinct haplotypes. Moreover, haplotype and nucleotide diversity in Ethiopian donkey populations were 0.903±0.032 and 0.020±0.003, respectively. A network analysis produced moderate star-like patterns suggesting past population demographic and spatial expansion. Population subdivision estimates demonstrated that Sinnar donkeys were considerably divergent from the other donkey populations. To trace the matrilineal genetic origin of Ethiopian donkeys, we retrieved 221 previously published domestic donkeys’ mtDNA D-loop sequences from the GenBank (146 from Chinese and 75 from worldwide domestic donkeys). The haplogroup derived from the Ethiopian sources formed the center of the network from which most of the worldwide domestic donkey populations emerged. This suggests that Ethiopia could be one of the centers of diversities for domestic donkeys in the Horn of Africa. The present study also overrides some previous reports that claimed donkeys were solely an Egyptian domesticate.

We quantified patterns of population genetic structure to help understand gene flow among elk populations across the Greater Yellowstone Ecosystem. We sequenced 596 base pairs of the mitochondrial control region of 380 elk from eight populations. Analysis revealed high mitochondrial DNA variation within populations, averaging 13.0 haplotypes with high mean gene diversity (0.85). The genetic differentiation among populations for mitochondrial DNA was relatively high (FST = 0.161; P = 0.001) compared to genetic differentiation for nuclear microsatellite data (FST = 0.002; P = 0.332), which suggested relatively low female gene flow among populations. The estimated ratio of male to female gene flow (mm/mf = 46) was among the highest we have seen reported for large mammals. Genetic distance (for mitochondrial DNA pairwise FST) was not significantly correlated with geographic (Euclidean) distance between

The endangered Grevy's Zebra (Equus grevyi) is confined to the Horn of Africa, specifically Ethiopia and Kenya. It is threatened by habitat loss and fragmentation due to human encroachment of historic range. Knowledge of population genetics is essential for the development of appropriate conservation actions and management. The focus of this study was to assess the heterogeneity and genetic distinctiveness of the two Grevy’s zebra populations in Ethiopia. Non-invasive fecal samples (N = 120) were collected during 2009–2010 from Grevy’s zebra populations in the Alledeghi Wildlife Reserve and the Sarite area, Ethiopia. Analyses of a 329 bp of the mtDNA control region of 47 sequences, revealed the existence of two unreported haplotypes in the northern population of Alledeghi, that were not shared with the southern population of Sarite. The Sarite population is contiguous with the Grevy’s zebra population in Kenya. The nucleotide diversity levels found in both the populations are extremely low.

Local domestic chicken populations are of paramount importance as a source of protein in developing countries. Bangladesh possesses a large number of native chicken populations which display a broad range of phenotypes well adapted to the extreme wet and hot environments of this region. This and the fact that wild jungle fowls (JFs) are still available in some regions of the country, it urges to study the present genetic diversity and relationships between Bangladeshi autochthonous chicken populations. Here, we report the results of the mitochondrial DNA (mtDNA) sequence polymorphisms analyses to assess the genetic diversity and possible maternal origin of Bangladeshi indigenous chickens. A 648-bp fragment of mtDNA control region (D-loop) was analyzed in 96 samples from four different chicken populations and one red JF population. Sequence analysis revealed 39 variable sites that defined 25 haplotypes. Estimates of haplotype and nucleotide diversities ranged from 0.745 to 0.901 and from 0.011 to 0.016, respectively. The pairwise differences between populations ranged from 0.091 to 1.459 while most of the PhiST (ΦST) values were significant. Furthermore, AMOVA analysis revealed 89.16 % of the total genetic diversity was accounted for within population variation, indicating little genetic differentiation among the studied populations. The median network analysis from haplotypes of Bangladeshi chickens illustrated five distinct mitochondrial haplogroups (A, D, E, F and I). Individuals from all Bangladeshi chicken populations were represented in the major clades D and E; those maternal origins are presumed to be from Indian Subcontinent and Southeast Asian countries, more particularly from South China, Vietnam, Myanmar and Thailand. Further, phylogenetic analysis between indigenous chicken populations and sub-species of red JFs showed G. g. gallus and G. g. spadiceus shared with almost all haplogroups and had major influence than G. g. murghi in the origin of indigenous chicken of Bangladesh. These results suggest that Bangladeshi indigenous chickens still have abundant genetic diversity and have originated from multiple maternal lineages, and further conservation efforts are warranted to maintain the diversity.

Donkeys are one of the least studied large domestic animals, even though they are economically important in many regions of the world. They are predominantly used as transport animals. Consequently, they are not kept in large numbers and this limits the number of archaeological specimens available for study. The donkey’s closest relative is the African wild ass, and genetic studies and zooarchaeological analyses of early donkeys indicate domestication of two genetically separate groups of wild asses in Africa. Maternal relationships revealed by mitochondrial DNA show that one group of donkeys was derived from the Nubian wild ass and that one was derived from an unknown ancestor distinct from the Somali wild ass.

Polymorphisms in the regulatory region of the CCR5 gene affect protein expression and modulate the progress of HIV-1 disease. Because of this prominent role, variations in this gene have been under differential pressure and their frequencies vary among human populations. The CCR2V64I mutation is tightly linked to certain polymorphisms in the CCR5 gene. The current Omani population is genetically diverse, a reflection of their history as traders who ruled extensive regions around the Indian Ocean. In this study, we examined the CCR2-CCR5 haplotypes in Omanis and compared the patterns of genetic diversity with those of other populations. Blood samples were collected from 115 Omani adults and genomic DNA was screened to identify the polymorphic sites in the CCR5 gene and the CCR2V64I mutation. Four minor alleles were common: CCR5-2554T and CCR5-2086G showed frequencies of 49% and 46%, respectively, whereas CCR5-2459A and CCR5-2135C both had a frequency of 36%. These alleles showed moderate levels of heterozygosity, indicating that they were under balancing selection. However, the well-known allele CCR5!32 was relatively rare. Eleven haplotypes were identified, four of which were common: HHC (46%), HHE (20%), HHA (14%) and HHF*2 (12%).

The Sultanate of Oman has a complex mosaic of livestock species and production systems, but the genetic diversity, demographic history or origins of these Omani animals has not been expensively studied. Goats might constitute one of the most abundant and important domestic livestock species since the Neolithic transition. Here, we examined the genetic diversity, origin, population structure and demographic history of Omani goats. Specifically, we analyzed a 525-bp fragment of the first hypervariable region of the mitochondrial DNA (mtDNA) control region from 69 Omani individuals and compared this fragment with 17 mtDNA sequences from Somalia and Yemen as well as 18 wild goat species and 1,198 previously published goat sequences from neighboring countries. The studied goat breeds show substantial diversity. The haplotype and nucleotide diversities of Omani goats were found equal to 0.983 ± 0.006 and 0.0284 ± 0.014, respectively. The phylogenetic analyses allowed us to classify Omani goats into three mtDNA haplogroups (A, B and G): haplogroup A was found to be predominant and widely distributed and accounted for 80% of all samples, and haplogroups B and G exhibited low frequencies. Phylogenetic comparisons with wild goats revealed that five of the native Omani goat populations originate from Capra aegagrus. Furthermore, most comparisons of pairwise population FST values within and between these five Omani goat breeds as well as between Omani goats and nine populations from nearby countries were not significant. These results suggest strong gene flow among goat populations caused by the extensive transport of goats and the frequent movements of human populations in ancient Arabia. The findings improve our understanding of the migration routes of modern goats from their region of domestication into southeastern Arabia and thereby shed light on human migratory and commercial networks during historical times.

Local chicken populations are a major source of food in the rural areas of South America. However, very little is known about their genetic composition and diversity. Here, we analyzed five populations from South America to investigate their maternal genetic origin and diversity, hoping to mitigate the lack of information on local chicken populations from this region. We also included three populations of chicken from the Iberian Peninsula and one from Easter Island, which are potential sources of the first chickens introduced in South America. The obtained sequencing data from South American chickens indicate the presence of four haplogroups (A, B, E and D) that can be further subdivided into nine sub-haplogroups. Of these, four (B1, D1a, E1a(b), E1b) were absent from local Iberian Peninsula chickens and one (D1a) was present only on Easter Island. The presence of the sub-haplogroups A1a(b) and E1a(b) in South America, previously only observed in Eastern Asia, and the significant population differentiation between Iberian Peninsula and South American populations, suggest a second maternal source of the extant genetic pool in South American chickens.

The study and conservation of endangered species is an important topic but collecting genetic samples is challenging as many of the threatened species are rare, elusive, or difficult to approach. Thus, the use of noninvasive samples to obtain genetic information has been gaining popularity. The noninvasive samples generally yield low DNA quantity and quality, which interferes with the genetic analyses performed. Several studies have identified factors that influence the amount and integrity of DNA extracted from noninvasive samples. Our work introduces a noninvasive DNA extraction method that can be modified and adapted to recover a large amount of DNA from stool samples. The protocol described here consists of two digestions and two purification steps and was tested on samples collected in the field from wild animals. This new method proved to be effective in the DNA extraction from scat samples in different conditions and from different species. The concentration of extracted DNA ranged from 30 to 70 ng/μl for Equus hemionus, Equus africanus, and Equus kiang. The success of mtDNA amplification ranged between 80 and 100% while for microsatellite markers the rate was between 65 and 100%. The reproducibility between scorings of the amplified fragments ranged between 76 and 100%. The current method has successfully improved the DNA yield on several species of wild equids. In addition to the classic genetic markers, we also test this method suitability for next-generation sequencing methods, by obtaining a RADseq library of 16 nM using 16 cycles and fragment size distribution similar to what is expected for high-quality samples. This protocol has successfully improved the DNA yield on different species by changing some steps of a classical spin-column DNA extraction protocol. We conclude that our fecal DNA extraction method can be used to provide DNA for a variety of downstream analyses.

Summary Among all livestock species, cattle have a prominent status as they have contributed greatly to the economy, nutrition and culture from the beginning of farming societies until the present time. The origins and diversity of local cattle breeds have been widely assessed. However, there are still some regions for which very little of their local genetic resources is known. The present work aimed to estimate the genetic diversity and the origins of Omani cattle. Located in the south-eastern corner of the Arabian Peninsula, close to the Near East, East Africa and the Indian subcontinent, the Sultanate of Oman occupies a key position, which may enable understanding cattle dispersal around the Indian Ocean. To disclose the origin of this cattle population, we used a set of 11 polymorphic microsatellites and 113 samples representing the European, African and Indian ancestry to compare with cattle from Oman. This study found a very heterogenic population with a markedly Bos indicus ancestry and with some degree of admixture with Bos taurus of African and Near East origin.

Utilizando un enfoque de encuestas estandar, se llevo a cabo una encuesta a nivel nacional para caracterizar morfologicamente e identificar las ecozonas de las poblaciones equinas caballares de Etiopia. Como consecuencia, se ha estudiado una nueva poblacion de caballos asilvestrados no investigada con anterioridad y otras siete poblaciones de caballos diferentes. Se estudio un total de diecisiete variables morfologicas en 503 caballos (293 sementales y 210 yeguas), pertenecientes a cinco de las ocho poblaciones equinas caballares identificadas. Las comparaciones multiples entre medias por pares (PMMC por sus siglas en ingles), utilizando un modelo lineal y analisis multivariantes, se realizaron por separado para cada sexo y los minimos cuadrados medios se utilizaron en el caso de los sexos agregados. Los resultados del PMMC mostraron que existian diferencias significativas (P < 0.05) entre las medias de la mayoria de las variables estudiadas. El analisis de los componentes principales mostro que la altura a la cruz, la altura al dorso, la altura a la grupa, longitud corporal, la longitud dorsal y la longitud ventral en conjunto representaban alrededor del 80 percent de las variaciones. Todas las distancias de Mahalanobis al cuadrado entre las poblaciones fueron significativas (P < 0.01). Las mayores diferencias fenotipicasfueron observadas entre las poblaciones equinas caballares de Bale y Selale y las menores entre las poblaciones Horro y Kafa. La funcion del analisis canonico discriminante mostro que el 77.05 percent de los individuos fueron clasificados correctamente dentro de sus respectivas poblaciones. Por otra parte, el analisis de agrupamiento, basado en las distancias de Mahalanobis al cuadrado, agrupo las cinco poblaciones equinas caballares estudiadas de Etiopia en tres grandes grupos y en cinco poblaciones de caballos diferentes.

This paper revises the evolutionary history of the stem root of the genus Equus from Eocene period (54 million years before present, MYBP) to present. It also assesses molecular taxonomy and evolutionary relationships of this line since the first appearance of fossil records in terrestrial deposits. Combining these two lines of evidences, we outline a more informative and consensus phylogeny in a more understandable context. We also compare and contrast evolutionary histories and phylogenetic relationships of equids inferred from paleontological as well as varieties of molecular data and their implications. Using pair-wise coalescence time estimates, we draw a consensus speciation order in the stem root of the genus Equus. With the help of molecular data, we suggest the reasons for enigmatic speciation events between asses and zebras as well as the backgrounds for genetic dissimilarities between hemiones of Asia and asses of Africa regardless their phenotypic similarities. Based on the evidences from molecular data and review of late Pleistocene megafauna extinction in the Americas, we believe that horses were certainly domesticated in the Eurasian Steppe or elsewhere that survived late Pleistocene megafauna's extinction than in the Americas. We discuss the true wild horse that was involved in horse domestication processes in line with recent evidences that unraveled multi-geographic origins and multi-maternal lineages in the present day domestic horses.

We carried out a nationwide survey to morphologically characterize and identify the geographic distribution of Ethiopian donkey populations. Here we re-evaluated some of the donkey populations previously identified and explored new ones from which we confirmed the existence of six distinct donkey populations and rejected one donkey population that was misidentified previously. We used twelve selected morphometric variables that recorded on a total of 569 adult donkeys (289 jacks and 280 jennets) spanning over wide arrays of ecologies in Ethiopia. Mean pairwise multiple comparisons (MPMC) between traits and multivariate analysis were carried out separately for jacks, jennets and aggregated gender. The MPMC showed significant differences between donkey populations for most of the traits studied. Principal component analysis showed that three body heights (height at wither, back and rump) and body length alone account for about 87.5% the total variations (eigenvalue = 10.49) of the 12 measured morphometric variables. Mahalanobis as well as Euclidean distances were also found to be highly significant ( P