Abstract:The dog mtDNA diversity picture from wide geographical sampling but from a small number of individuals per region or breed, displayed little geographical correlation and high degree of haplotype sharing between very distant breeds. For a clear picture, we extensively surveyed Iranian native dogs (n = 305) in comparison with published European (n = 443) and Southwest Asian (n = 195) dogs. Twelve haplotypes related to haplogroups A, B and C were shared by Iranian, European, Southwest Asian and East Asian dogs. I… Show more
“…3 ). The relatively high haplotype (0.86 ± 0.04) diversity is comparable to genetic diversity indices reported from modern native breeds from Portugal and Iran 75 , 76 . Figure 3 Median-Joining Network of Roman (n = 45) and modern (n = 34) mtDNA sequences (82 bp).…”
Several dog skeletons were excavated at the Roman town of Augusta Raurica and at the military camp of Vindonissa, located in the northern Alpine region of Switzerland (Germania Superior). The relationships between them and the people, the nature of their lives, and the circumstances of their deaths are unclear. In order to gain insight into this dog population, we collected 31 dogs deposited almost simultaneously in two wells (second half of the third century CE), three dogs from burial contexts (70–200 CE and third to fifth century CE) at Augusta Raurica, and two dogs from burial contexts at Vindonissa (ca. first century CE). We detected a mixed population of young and adult dogs including small, medium and large sized individuals. Three small dogs had conspicuous phenotypes: abnormally short legs, and one with a brachycephalic skull. Stable isotope analysis of a subset of the dogs showed that their diets were omnivorous with a substantial input of animal proteins and little variation, except one with a particularly low δ15N value, indicating a diet low in animal proteins. Partial mitochondrial DNA sequences from 25 dogs revealed eight haplotypes within canine haplogroup A (11 dogs; 44%; 5 haplotypes), C (8 dogs; 32%; 1 haplotype), D (4 dogs, 16%; 1 haplotype) and B (2 dogs, 8%; 1 haplotype). Based on shotgun sequencing, four Roman mitogenomes were assembled, representing sub-haplogroups A1b3, A1b2 and C2. No canine pathogens were identified, weakening the assumption of infectious disease as a cause for dog disposal. The genetic and morphological diversity observed in dogs of Augusta Raurica and Vindonissa is similar to modern dog diversity.
“…3 ). The relatively high haplotype (0.86 ± 0.04) diversity is comparable to genetic diversity indices reported from modern native breeds from Portugal and Iran 75 , 76 . Figure 3 Median-Joining Network of Roman (n = 45) and modern (n = 34) mtDNA sequences (82 bp).…”
Several dog skeletons were excavated at the Roman town of Augusta Raurica and at the military camp of Vindonissa, located in the northern Alpine region of Switzerland (Germania Superior). The relationships between them and the people, the nature of their lives, and the circumstances of their deaths are unclear. In order to gain insight into this dog population, we collected 31 dogs deposited almost simultaneously in two wells (second half of the third century CE), three dogs from burial contexts (70–200 CE and third to fifth century CE) at Augusta Raurica, and two dogs from burial contexts at Vindonissa (ca. first century CE). We detected a mixed population of young and adult dogs including small, medium and large sized individuals. Three small dogs had conspicuous phenotypes: abnormally short legs, and one with a brachycephalic skull. Stable isotope analysis of a subset of the dogs showed that their diets were omnivorous with a substantial input of animal proteins and little variation, except one with a particularly low δ15N value, indicating a diet low in animal proteins. Partial mitochondrial DNA sequences from 25 dogs revealed eight haplotypes within canine haplogroup A (11 dogs; 44%; 5 haplotypes), C (8 dogs; 32%; 1 haplotype), D (4 dogs, 16%; 1 haplotype) and B (2 dogs, 8%; 1 haplotype). Based on shotgun sequencing, four Roman mitogenomes were assembled, representing sub-haplogroups A1b3, A1b2 and C2. No canine pathogens were identified, weakening the assumption of infectious disease as a cause for dog disposal. The genetic and morphological diversity observed in dogs of Augusta Raurica and Vindonissa is similar to modern dog diversity.
“…Consequently, one of the notable viewpoints on the primary location of the dog domestication has been the Southwest Asia, likely the Middle East [ 1 ]. Moreover, the Middle East has been included in the considerable allelic distribution between dog breeds and wolf [ 10 ]; however, this presumption has been queried because of dog-wolf hybridization as stated in previous studies [ 11 – 13 ]. The dog is a considerable example of phenotypic variation under artificial selection and demographic forces, but genetic basis of this diversity is not yet completely clear.…”
Section: Objectivementioning
confidence: 99%
“…Finally, we compared the effect of variome between the dog and wolf genomes using Sorting Intolerant from Tolerant (SIFT) algorithm [ 19 ], Ensembl annotation [ 22 ] and DAVID [ 23 ] tool [ 14 ]. The data presented herein together with our previously mitochondrial DNA sequence on Iranian dogs [ 11 ] will provide useful resources to understand genetic structure of the Iranian dogs and testing hypotheses on the dog origin and domestication issues.…”
Objective
The data provided herein represent the whole-genome resequencing data related to three wolves and three Iranian local dogs. The understanding of genome evolution during animal domestication is an interesting subject in genome biology. Dog is an excellent model for understanding of domestication due to its considerable variety of behavioral and physical traits. The Zagros area of current day Iran has been identified as one of the initial centers of animal domestication. The availability of the complete genome sequences of Iranian local canids can be a valuable resource for researchers to address questions and testing hypotheses on the dog domestication process.
Data description
We collected blood samples from six Iranian local canids including two hunting dogs (Saluki breed), a mastiff dog (Qahderijani ecotype) and three wolves. We extracted genomic DNA from blood samples. Sequence data were produced using the Illumina HiSeq 2500 system. All sequence data are available in the National Genomics Data Center (NGDC), Genome Sequence Archive (GSA) database under the accession of CRA001324 and the National Center for Biotechnology Information (NCBI) under the accession of PRJNA639312. The short-read sequences with the mean depth of 16X were aligned to the dog reference genome (CanFam3.1) and achieved 99% coverage of the reference assembly. The obtained information from this experiment will be useful in evolutionary biology.
“…Therefore, one of the most theories about the geographical origin of the domestic dog has been that they originated in Southwest Asia, presumably in the FC [21]. In addition, the Middle East has been proposed as the beginning of domestic dog for great haplotype sharing between wolves and dog breeds [69] although this hypothesis has been questioned due to dog-wolf introgression [7,8,30] rather than an indication of Middle Eastern origins. The dog is a notable instance of variation under domestication, however the evolutionary processes underlying the genesis of this diversity are weakly realized.…”
Background: Advances in genome technology have simplified a new comprehension of the genetic and historical processes crucial to rapid phenotypic evolution under domestication. To get new insight into the genetic basis of the dog domestication process, we conducted whole-genome sequence analysis of three wolves and three dogs from Iran which covers the eastern part of the Fertile Crescent located in Southwest Asia where the independent domestication of most of the plants and animals has been documented and also high haplotype sharing between wolves and dog breeds has been reported. Results: Higher diversity was found within the wolf genome compared with the dog genome. A total number of 12.45 million SNPs were detected in all individuals (10.45 and 7.82 million SNPs were identified for all the studied wolves and dogs, respectively) and a total number of 3.49 million small Indels were detected in all individuals (3.11 and 2.24 million small Indels were identified for all the studied wolves and dogs, respectively). A total of 10, 571 copy number variation regions (CNVRs) were detected across the 6 individual genomes, covering 154.65 Mb, or 6.41%, of the reference genome (canFam3.1). Further analysis showed that the distribution of deleterious variants in the dog genome is higher than the wolf genome. Also, genomic annotation results from intron and intergenic regions showed that the proportion of variations in the wolf genome is higher than that in the dog genome, while the proportion of the coding sequences and 3′-UTR in the dog genome is higher than that in the wolf genome. The genes related to the olfactory and immune systems were enriched in the set of the structural variants (SVs) identified in this work. Conclusions: Our results showed more deleterious mutations and coding sequence variants in the domestic dog genome than those in wolf genome. By providing the first Iranian dog and wolf variome map, our findings contribute to understanding the genetic architecture of the dog domestication.
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