Brian Chen
Professor Jobin
ANTH 1
May 14, 2016
Scientific Journal Article Review
Introduction:
This study is one that determines whether or not the “IGF1 small dog haplotype is derived from Middle Eastern grey wolves” [Gray et al. 2010]. According to the article the similar to insulin growth factor 1 called in this article the IGF1 gene is connected to the variation of sizes in domestic dog breeds. Apparently, in all small breeds, a SINE element and single nucleotide polymorphism can be found in “Intron 2 of IGF1” [Gray et al. 2010], this element is also absent in most large breeds of dogs. In order to gain a better understanding of the ancestry behind the variation patterns of IGF1, the team consisting of Melissa M. Gray, Nathan B. Sutter, Elaine A. Ostrander, and Robert K. Wayne conducted a survey to a large portion of the grey wolf populations.
Background:
According to this article, domestic dogs have a massive amount of diversity in their phenotypes in terms of “coat colour, skeletal proportion, and behavior” [Gray et al. 2010]. Apparently, for those devoted to the study of the “evolutionary history of domestic dogs and the genetic basis for phenotypic traits” [Gray et al. 2010], understanding what exactly caused this diversity is a major form of motivation for them. So far, it’s been found that the domestic dog’s common ancestor was the grey wolf. Furthermore, according to molecular genetic evidence, there seems to have been several interbreeding and domestication events between grey wolves and domesticated dogs. However, it seems that it is uncertain where and when exactly the dog originated from. There are conflicts in results from various attempts with varying methods. Results from mitochondrial DNA sequencing shows that domesticated dogs may have come from East Asia between 5,000 and 16,000 years ago, while using archaeological studies show results that suggest they came from either the Middle East, Western Russia, or even Europe between 14,000 and 31,000 years ago.
The goal of the lab is to find and understand what exactly is the molecular mechanism that caused domestic dogs to have a large diversity in size. It was discovered by the team previously that there was a haplotype on chromosome 15 that was found mainly in smaller sized dogs with the characteristic of affecting size. Another haplotype was found in the IFG1 gene to associate with skeletal size while using fine mapping revealed that “a ~75 kb selectively swept haplotype [was] most strongly associated with size variation” [Gray et al. 2010]. Furthermore, markers were found on this haplotype to be fixed within a large portion of small sized and genetically related breeds of dogs and almost absent from larger dog breeds. Curiously, this gene found in small sized dogs wasn’t found in any wild dog species surveyed such as grey wolves. But, other than this gene, no other attempts at characterizing the genetic variances in IGF1 was ever done before, leading to this lab’s purpose, to discover what “ancestral pattern[s] of variation” [Gray et al. 2010] there are in the IGF1 gene through the surveying of various grey wolf populations around the world.
Methods:
Microsatellite, SNP, and SINE (short interspersed elements) markers within IGF1:
From what the article tells us,
SNP Genotypes:
The article says that the team, for the purpose of investigating “the evolutionary history of the IGF1 locus and the origin of the haplotypes found in domestic dogs” [Gray et al. 2010], they used principal components analysis (PCA) on the genotypes found on “94 dog-derived SNP markers spanning the IGF1 interval” [Gray et al. 2010]. On the very first PCA axis, in terms of species, domestic dogs were found to have a clear-cut difference from their wilder ancestors, the grey wolves and coyotes. On their second PCA axis, the team tried to analyze the difference between large and small sized dog breeds as well as “to a lesser extent between New World and Old World grey wolves” [Gray et al. 2010]. On this second axis, they found fruitful results. Akita dogs, a domesticated breed of dog from ancient times was positioned between grey wolves and the main group of domestic dog breeds. Outliers like the Rottweiler and Mastiff, which were well known as large dog breeds were found within a group of small dog breeds. They were found to have unexpectedly similar genetics within the IGF1 gene. The rest of their results from the PCA method included the discovery that dog breeds that were “homozygous for the four most common of the IGF1 20 SNP marker haplotypes” [Gray et al. 2010] were comparable to grey wolf and coyote haplotypes that were homologous. The haplotypes of the wolves that were shown to be the most similar to small dog breeds were found in those living in Spanish and Israeli areas. This confirmed the hypothesis that the team came up with ‘that Middle East and Spanish wolves [had] haplotypes closest to those of small dogs” [Gray et al. 2010].
Long Sequence (6331 bp):
In order for the team to progress further in characterizing the variation of the IGF1 gene within grey wolf populations, they “sequenced 6331 base pairs (bp) of intron 2 that directly surrounded the diagnostic ‘small’ SNP locus and the SINE element” [Gray et al. 2010]. They managed to identify 13 private alleles and 20 polymorphic loci within grey wolf populations, 12 and 11 with in coyote populations, and 2 and 2 within domestic dogs. Utilizing this method, the results revealed that Israeli wolves in terms of haplotypes, had the most in common with domestic dog breeds, differing by only “3 to 4 substitutions” [Gray et al. 2010]. A network constructed of these differences presented a similar connection between the Israeli wolves and the domestic dogs’ haplotypes. With standard deviation, the scientists found that as a result, “nucleotide diversity was highest in coyote” [Gray et al. 2010], second highest in grey wolves from Europe, and third highest in grey wolves from Israel.
Short Sequence (4811)
The lab team created a tree topology from the sequence data to find the common connections between the haplotypes of small sized domesticated dog breeds and their wild ancestors, the grey wolves. The results supported the “close affinity between the small dog haplotype and those of Middle Eastern grey wolves” [Gray et al. 2010] that were the results of examining the 6331 base pairs long sequence. But in order to make sure that there was no influence by limited samples in the tree topology, the team surveyed and sequence 8 more grey wolf populations “for a subset of the amplicons” [Gray et al. 2010]. The reason the team chose amplicons was so that they could keep the cost at a minimum while maximizing the amount of markers that were discovered previously and could be sequenced. Based on “28 SNPs and two indels, 21 haplotypes and three novel SNPs were identified” [Gray et al. 2010]. One of them was found only in coyotes, one was only in grey wolves from Israel, and another was found to be in wolves located in Alaska, Israel, Russia, and Mexico. Another result of the sequencing was the finding that wolf haplotypes from wolves in Israel, India, and Iran had the most in common with haplotype 4 in common dog breeds of small size with a difference of only 1 to 3 substitutions. This was further supported by a neighbor-joining tree topology that showed the same results. This again confirms the team’s previous observations of a common and deep ancestry between small dog breeds and wolves from the Middle East.
Constraint Trees:
The team decided that to verify even further the phylogenetic trees’ topology that resulted with the common link between the haplotypes of small dogs and Middle Eastern grey wolves, they had to build constraint trees “for the long and short sequence data” [Gray et al. 2010]. Within those trees, the common haplotype found in small breeds of domestic dogs was clustered with haplotypes found in large dog breeds. For both the long sequence and the short sequence, 3 constraint trees each, were built where a small dog haplotype was made to be a sister to other haplotypes. As a result, the team confirms by analyzing the constraint trees “that the likelihoods of the unconstrained trees were significantly better in all comparisons” [Gray et al. 2010].
Recombination:
In past research, “a recombination point just 5’ of the diagnostic SNP locus” [Gray et al. 2010] was found to actually a critical locus between haplotypes of common and minor small dog breeds. The team also found that in their graphs of ancestral reconstruction, there was an analogous recombination point with similar properties “between CanFam1 position 44230920 and 44231095” [Gray et al. 2010]. To investigate what effect recombination probably had on their researched tree topology, they built neighbor-joining trees for both the long and short sequence datasets that analyzed both sides of their recombination points. The results the team found were that on the 3’ side in the long sequence dataset, the haplotypes of Israeli grey wolves were ancestral to the haplotypes of small dog breeds while in the short sequence dataset, the haplotypes of all small dog breeds were ancestral to all dogs. Meanwhile on the 5’ side, “all but the common small dog haplotype” [Gray et al. 2010] as well as a great deal of the haplotypes of Israeli grey wolves “clustered with support values of 97%” [Gray et al. 2010] on the long sequence dataset and 88% on the short sequence data set.
Results/Discussion:
Work from the past seems to have already labeled IGF1 as an important gene that affects skeletal size in domesticated dogs. The team, consisting of Melissa M. Gray, Nathan B. Sutter, Elaine A. Ostrander, and Robert K. Wayne investigates the domestic dog’s ancestors’ genetic variation within the IGF1 gene for the purpose of revealing the gene’s evolutionary history. The study confirms that “the absence of the derived small SNP allele in the intron 2 region of IGF1” [Gray et al. 2010] within the sampled grey wolf populations. This also grounds the wild canines’ as well as a majority of large dog breeds’ absence of the SINE element associated with small dog breeds. The lack “of both the SINE element and SNP allele” [Gray et al. 2010] within the ancestors of domestic dogs like grey wolves makes it a possibility that the genetic mutation that caused dogs to have smaller bodies happened after the domestication of dogs, meaning that the mutation was a unique event of genetic recombination that happened within domesticated dog breeds. However, evidence regarding the recombination event happening within domestic dogs had not been found and because all dog breeds of small size possessed these mutations, the phenotype concerning small size probably happened in the early history of dog domestication.
Even though allele that distinguish small and large domestic dog species have been found, the exact genetic cause has not been identified. Through the team’s use of electrolysis in tracking microsatellite mutations, it’s been proven a possibility that “the microsatellite located in the promoter region of IGF1” [Gray et al. 2010] may have been the cause, but the allelic range that was examined in domestic dog breeds of both small and large size was found to have similarities to the the allelic range in grey wolves and coyotes, disproving this hypothesis.
Work Cited:
Online Citation: Gray, Melissa M., Nathan B. Sutter, Elaine A. Ostrander, and Robert K. Wayne. "BMC Biology." The IGF1small Dog Haplotype Is Derived from Middle Eastern Grey Wolves. BioMed Central, 24 Feb. 2010. Web. 19 May 2016. <http://bmcbiol.biomedcentral.com/articles/10.1186/1741-7007-8-16>.
Journal Citation: Gray, Melissa M., Nathan B. Sutter, Elaine A. Ostrander, and Robert K. Wayne. "The IGF1 Small Dog Haplotype Is Derived from Middle Eastern Grey Wolves." BMC Biology BMC Biol 8.1 (2010): 16. Web.