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Evolutionary forces during domestication process and breed formation have led to remarkable differences between wild and domestic sheep genomes. In this study, we compared genetic diversity of 13 Iranian Mouflons (Ovis orientalis) and 20 Iranian domestic sheep (Ovis aries) based on 86 candidate genes putatively involved in the domestication of sheep. Mean nucleotide diversity and mean expected heterozygosity of candidate genes calculated by means of VCF tools and statistical analysis were performed via IBM SPSS software. Our results showed that Mouflon was superior for both calculated diversity parameters in the majority of candidate genes under study. In fact, wild group showed higher mean nucleotide diversity and mean heterozygosity in 69 (32 statistically significant) and 49 (entire statistically significant) candidate genes, respectively. Candidate genes corresponding to immune responses, growth, and meat production traits had the most prominent differences between Mouflon and domestic sheep. Based on our results, a decrease in genetic diversity of candidate genes in domestic sheep must be considered in conservation genetics and additionally designing conservation genetic strategies in order to preserve genetic resources of Iranian wild and domestic sheep, which is essentially needed.

The Asiatic cheetah (Acinonyx jubatus venaticus), has disappeared in major parts of its mountainous habitats in west Asia. Asiatic cheetah is a critically endangered subspecies currently found only in central Iran. In this study, the feeding habits of Asiatic cheetah was investigated in two reserves in central Iran. Diet and prey selection of cheetah were assessed using two biomass models along with Jacob's selectivity index. We found no significant difference between biomass consumption based on each model between the reserves or between models inside each reserve. Over 90 % of species diet was composed of three medium-sized ungulates (i.e. 15–40 kg): wild sheep, wild goat and chinkara. Hares and other small mammals (less than 15 kg) made up the remainder of their diet. Asiatic cheetahs mainly preyed on wild sheep (Ovis vignei) which composed more than 50 % of consumed biomass. Wild sheep was identified as single staple prey, while chinkara (Gazella bennettii) was the most preferred prey despite its lower occurrence. Our study indicates that wild sheep, wild goat and especially chinkara are critical for persistence of Asiatic cheetah and must be particularly considered in conservation plans.

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.

Evaluation of habitat sustainability indexes is essential in wildlife management and conservation of rare species. Suitable habitats are required in wildlife managements and conservation also, they increase reproduction and survival rate of species. In this study in order to mapping habitat sustainability and recognizing habitat requirements of Iranian Cheetah (Acinonyx jubatus venaticus), field data from Dare Anjir wildlife refuge were collected since autumn 2009 until summer 2011. Ecological Niche Factor Analysis approach has been used to develop habitat suitability model. In this method primary maps of habitat variables including elevation, slope, aspect, vegetation cover, distance from water sources and environmental monitoring stations have been produced by Idrisi and Biomapper software and imported in Biomapper. The output scores obtained from the analysis showed that Iranian cheetah tends to mountain areas where has more topographical features for camouflage in order to hunting, and northern aspects which have more humidity, denser vegetation cover and more preys . Our result showed that the Iranian cheetah has medium niche width and prefer marginal habitats.

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species., M.N.-S. and Q.N. are funded by the CSIRO Science Excellence Research Office. M.P.-E. was funded by a CSIRO McMaster Visiting Fellowship. Mouflon genome sequences were generated by the NextGen Consortium, as part of the European Union’s Seventh Framework Programme (FP7/2010-2014 grant 244356).

Background The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA). Results We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12–10 ka ago. Conclusions Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2342-2) contains supplementary material, which is available to authorized users.

Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Argonaute proteins were highly conserved across plant kingdom. Phylogenic analysis divided plant Argonautes into three classes. Argonaute proteins have three conserved domains PAZ, MID and PIWI. In addition to three conserved domains namely, PAZ, MID, and PIWI, we identified few more domains in AGO of some plant species. Expression profile analysis of Argonaute proteins showed that expression of these genes varies in most of tissues, which means that these proteins are involved in regulation of most pathways of the plant system. Numbers of alternative transcripts of Argonaute genes were highly variable among the plants. A thorough analysis of large number of putative Argonaute genes revealed several interesting aspects associated with this protein and brought novel information with promising usefulness for both basic and biotechnological applications.