Ben Grissom.110/14/98

Annotated bibliography

A. Katya, T.R. Famula, R.L. Bettinger 2012 Pathways to Animal Domestication. In Biodiversity . in Agriculture: Domestication, Evolution, and Sustainability, pp. 227-229. Cambridge . University Press, Cambridge

This source provides a theory that there are multiple ways for an animal to become domesticated. In every path, it is recognized that domestication is a process, not a spontaneous occurrence. Some theories support the idea that humans do most of the work domesticating, but many others disagree, stating that the animals do more work becoming domesticated, and others yet lend backing to the theory that domestication is a mutual relationship between the two. The journal also supports the idea that people domesticate based on behavioral aspects. The author states what she believes to be a set list of traits which are looked for in a species in candidacy for domestication. She says that an animal which will have less change in its domesticated habitat is more fit to be domesticated, and will be domesticated more quickly. Zeder believes the primary change in a domesticated animal is it's reformed brain and its reduced size. The morphological and physical changes are the secondary factors, only afterthoughts of the taming of a species. She believes that the difference between a tame and domesticated animal is that a domesticated animal cannot truly turn back to its fore-generations' ways of life. She says feral animals cannot live the same way there wild counterparts do.

This source provides many new and intriguing theories about domestication. It is a valuable aid to my research question, and when it come time, my thesis. This source would be quite useful to anyone curious about the various routes as to which an animal may become domesticated, as it explains this clearly and concisely.

Albert FW, Somel M, Carneiro M, Aximu-Petri A, Halbwax M, et al. (2012) A Comparison of Brain Gene Expression Levels in Domesticated and Wild Animals. PLoS Genet 8(9): e1002962. doi:10.1371/journal.pgen.1002962

This article introduces a theory that the tame and docile behavior of domesticated animals is entirely based in neural DNA. The study included four wild species and there domestic counterparts, as well as two strains of rats, one bred for aggression and the other for tameness. In each analysis of two similar species, the "mRNA sequencing" is compared in order to determine whether there are correlations and mutations in the domesticated subjects. The study, once complete, showed that there was in fact little correlation and change of mRNA sequencing in the

domesticated species. While variation has occurred, it has not shown to be any greater than what is expected by chance as one species diverges fr

om another, except between dogs and wolves. Some notable changes that do not relate to neural function including mutations causing: dogs to produce energy less efficiently, greater levels of glucose in the bloodstream of pigs, and greater adhesion of cells in rabbits. Overall, the theory is proven null, but there are still valuable findings of which to take note.

This article provided evidence against the theory of neural DNA causing domesticated behavior. The research helped answer the question of how neural DNA impacts behavior and also other effects of neural DNA on a domesticated animal. It provided insight into some lesser known physical changes in different domesticated species. This source can be used to discredit the theory that neural DNA impacts domesticated behavior.

Nelson, A. (2004). Development of the Domestic Donkey. Science, 305, 1781-1781.

This source discusses the genetic origins of the donkey, equus asinus. Donkeys are an interesting source of study because they are one of the few species not bred for the sustenance of people, but instead for their strength. The researchers found that the domestication of donkeys coincided with the rise of mass transportation, so the genes manipulated in breeding were primarily strength and endurance. The researchers found that the progenitors of the donkeys came from Africa, a bustling area at the time of domestication, and the link in variability between various domesticated species. The two progenitors were the Nubian wild ass from north central Africa and the Somali wild ass from northeastern Africa. Researchers also found that there were multiple separate incidences of the domestication of donkeys from already genetically different populations of asses. The greatest source of variation was in the MC15T gene, a gene related to nutrient digestion. This gene was likely changed because the different populations of donkeys, which developed in different parts of the world, eat different foods and need to digest there food differently.

This source supports the theory of morphological development as everything which changed in the donkeys is a direct result of human breeding. This source answers the question of where donkeys came from. The source would be useful to anyone studying the history of transportation or the genetics of domestication.

Carneiro, M., Afonso, S., Geraldes, A., Garreau, H., Bolet, G., Boucher, S., ... Ferrand, N. (2011). The Genetic Structure of Domestic Rabbits. Molecular Biology and Evolution, 28(6), 1801-1816. Retrieved December 10, 2014, from http://mbe.oxfordjournals.org/content/28/6/1801.full.pdf . htmlThis source evaluates the genetic structure of several different varieties of domesticated

rabbits, such as the Belgian Hare, Champagne Silver, English Lop, and Rex. The researchers determined that all of these diverse, beautiful (and soft) breeds came from one point of origin. They believe that all the species originate from the European Rabbit. They are also a very recently domesticated species, and show surprisingly high genetic diversity for having been domesticated so recently. It is also recognized that the European Rabbits gene has been bred

back into the rabbit gene pool as decades have progressed. It is an unusual occurrence for all animals of a domesticated species to come from one origin, rather than several independent incidences of domestication, as has occurred with the equine, bovine and porcine species. Another uncommon trait of this species is that its ancestor, the European Rabbit, is not only still alive, but thriving, whereas most other specie’s ancestors are extinct. Researchers also found a severe bottleneck in the domestication of rabbits which occurred during the French revolution. This caused a lot of inbreeding, drastically changing the genetic composure of the species, and muddying the researcher’s ability to determine what precisely was natural selection and what was artificial alteration through domestication.

This source supports the domestication syndrome, as it describes indirect alterations to the specie’s genes which the domesticators did not intend to have occur. It is a valuable search to anyone studying the origin of rabbits or the modern domestication of a species. This source answers questions about how animals become domesticated.

(2014). Chicken Photo

Subramanya, C. K. (Photographer). (2012, October 30). Red jungle fowl [Print Photo]. Retrieved from http://commons.wikimedia.org/wiki/File:Red_jungle_fowl.png

The sources being compared in this annotation are the domesticated chicken and its ancestor, the red jungle fowl. Let it be known that these images are not to scale and may only be compared in a qualitative or proportional fashion. The most obvious of differences is the uniformity of color in the modern domesticated chicken’s coat, as opposed to the decorative contrast of the jungle fowl’s coat, most likely developed so that it might attract mates in the wild. Another difference is the extensive length of the posterior feathers of the red jungle fowl, as opposed to the domesticated chicken’s rather short rear feathers. This, once again, is most likely a present feature in the jungle fowl because its sole purpose is to find a mate and reproduce. The beak of the jungle fowl is slightly shorter than of its domesticated counterpart. This could perhaps be a result of a different diet for the domesticated chicken which caused this specie’s beak to lengthen.

This source supports the theory of the domestication syndrome because the loss of all of these decorative features was not the direct intention of the domesticator. This source is valuable to anyone trying to find out more about how chickens have become what they are. It answers questions about what domestication does to a species.

Clare, K. (Photographer). (2007, August 6). Feral Cats of tarragona [Web Photo]. Retrieved from https://www.flickr.com/photos/kenclareblog/1152473128/

Wayne. (Photographer). (2013, September 06). The African Wildcat [Web Photo]. Retrieved from https://ferrebeekeeper.wordpress.com/2013/09/06/

This is a comparison of a photo of a domesticated cat to its nearest ancestor, the African Wild Cat. As these two photos are not scaled, only qualitative and proportional comparisons may be made. The two images being compared are attached below. The African Wild cat has a much sharper set jaw than the domestic cat and the domestic cats overall facial structure is much rounder. The eyes of the domesticated cat are much rounder and more ovular than than the African Wild Cat’s, which are lemon shaped. The Wild Cat has a much leaner build with thinner legs. The tail, however, appears much thicker in the Wild Cat than in the domesticated cat. The gaskin of the Wild Cat’s hind leg seems to be much longer than that of the domesticated cat’s, but they both seem to have a similarly proportioned lower leg. While the back of the domesticated cat arches, the back of the African Wild Cat is concave. The top of the domesticated cat’s head is flatter than that of the Wild Cat’s. The belly markings of the domesticated cat are more distinct than those of the wild cat.

These images provide valuable source of information which supports the domestication syndrome. Many of the differences which appeared in the domesticated cat seem to have physical no purpose for which they were directly developed and seem to have therefore developed simply because of domestication. These images would be valuable for anyone interested in cat’s origins or there unique traits. They answer questions about how animals change when they are domesticated.

African Wild Cat

Domesticated Cat

Elisson, A. (2004). African Origins of the Domestic Donkey. Science, 304, 1781-1781.

This source discusses the genetic origins of the donkey, equus asinus. Donkeys are an interesting source of study because they are one of the few species not bred for the sustenance of people, but instead for their strength. The researchers found that the domestication of donkeys coincided with the rise of mass transportation, so the genes manipulated in breeding were primarily strength and endurance. The researchers found that the progenitors of the donkeys came from Africa, a bustling area at the time of domestication, and the link in variability between various domesticated species. The two progenitors were the Nubian wild ass from north central Africa and the Somali wild ass from northeastern Africa. Researchers also found that there were multiple separate incidences of the domestication of donkeys from already genetically different populations of asses. The greatest source of variation was in the MC15T gene, a gene related to nutrient digestion. This gene was likely changed because the different populations of donkeys, which developed in different parts of the world, eat different foods and need to digest there food differently.

Fang, M., Larson, G., Ribeiro, H., Li, N., Andersson, L., & Barsh, G. (2009). Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs. PLoS Genetics, E1000341-E1000341. Retrieved October 8, 2014, from PLOS Genetics.

This source identifies the variations of coat colors in pigs and how they have developed. As supported by other sources, these developments have occurrs through mutations of the "MC1R gene"; This mutation causes piebald colorations and lighter colorations in many species of domesticated animals. Coloration distribution differed between breeds of pigs that had been long separated. Domesticated species are far more likely to develop heterozygous coloration traits. Wild boars are almost always black, while European are most likely pinto. Indonesian breeds have a relatively even distribution of coloration. There are many different halotypes in the "MC1R gene" which impact the coloration of an animal, but these researchers have narrowed down that number significantly, determining which halotypes remain the same throughout all breeds. The coloration differences are also a signal of how close or distant each porcine breed is, along with other signals such as genetic variation and regional location.

This source provides evidence supporting the theory that animals become domesticated based on morphological alterations, going into great depth and describing how colors are changed as an animal becomes domesticated. It answers questions such as what parts of the MC1R gene cause changes in coloration in a domesticated species. This resource would be useful for anyone interested in how domesticated animals develop alternate colorations.

Ghosh S, Qu Z, Das PJ, Fang E, Juras R, et al. (2014) Copy Number Variation in the Horse Genome. PLoS Genet 10(10): e1004712. doi:10.1371/journal.pgen.1004712

The source compares a series of genomes of 38 healthy horses and six horses with congenital diseases along with a Prezwalski's horse against the thoroughbred genome for copy number variations (CNV's). CNV's are variations in an animal's genome which differ from the normal number of copies in a genome. This requires a control genome to compare other genomes of the species to. The American Quarter Horse had the least CNV's in comparison to the thoroughbred with an average of 15.667, as one knowledgeable of horse breeds might expect since they were both bred from the Arabian horse. The breed with the greatest number of CNV's was the American miniature pony, a peculiar breed which is different appearance wise in most every way from a thoroughbred horse. These CNV's indicate how far away each breed has drifted from the thoroughbred species or vice versa; the most important CNV value is that between the Prezwalski's horse and the Thoroughbred. The variation was similar to that of native ponies and draft horses, but this variation demonstrates how much the thoroughbred has drifted from its ancestor, most closely represented by the Prezwalski's horses. The values of these CNV's were an average of 21.

This source provided insight into how selection has caused variation within a species and how genetics have played a role in that variation. This source would be beneficial to anyone curious as to how much breeds of horses have varied or the genetics behind it. It supports the theory that genetics play the primary role in domestication, not another outside factor.

Giuffra, E., Kijas, J., Amarger, V., Carlborg, O., Jeon, J., & Andersson, L. (2000). The Origin of ‘ the Domestic Pig: Independent Domestication and Subsequent Introgression. Genetics Society ` of America, 154(4), 1785-1791. (2000, April 1). Retrieved September 16, 2014, from . Genetics.org.

The information presented gives a detailed account of the variable genetic compositions of certain sections of the porcine genome in pigs of the following origins: European, Asian, Asian introgression into European, and a pig from the Cook Islands. The sections studied included the "mtDNA cytochrome B", the "hypervariable mtDNA control region", the melanocortin receptor (MC1R, which has to do with coloration,) tyrosinase, and GPIP. They are all being observed for the same thing: Variance. In the Asian pigs, and certain European pigs, black coloration coded on the MC1R gene varied a surprisingly large amount from all other varieties of European pigs. One important but unfortunate piece of information to note is that no information was found on how modern domesticated pigs vary from the body structures of their ancestors. The "mtDNA" of Italian pigs was surprisingly different from any other breed across Eurasia, possibly due to almost 2000 years of isolation. The extreme genetic variances between some varieties of these pigs are thought to be due to the intensive selective breeding that has taken place for almost 9,000 years as each variety of pig has been bred and is still bred for a specific set of traits.

This article showed how much variation can occur in domesticated breeds, even within one species. The research helped answer questions about what isolation and introgression can do to cause genetic variation in a species; also, it introduced new DNA sections commonly altered in domestication. One can use this information to support the possible variations that may occur in a domesticated species.

Glazko, Valeriy, Zybaylov, Boris, Glazko, Tatiana. Domestication and Genome Evolution. International Journal of Genetics and Genomics. Vol. 2, No. 4, 2014, pp. 47-56. doi: 10.11648/j.ijgg.20140204.11

This source discusses a new, original theory on domestication in which a specie’s tendencies for subgenomes to develop determines its likelihood to be domesticated. The researchers focused specifically on genomic research of various large mammals, such as pigs, cows, and sheep. The researchers found that these subgenomes which allow for greater variation occur in sections of the genome which influenced the immune system, metabolism, and development of retrotansposons, sections of RNA which are also subject to mutation. One theory behind why the increase in retrotransposons developed is that when the animals stayed in one area they were exposed to the areas pathogens, and the inbreeding of these small populations activated the mutations within the retrotransposons. The researchers also found that in order for an animal to be domesticated, there must be a high degree of genetic variability naturally occurring in the genome. If this is not the case, the animals will not naturally adapt to their rapidly changing surroundings. The animals must also have strong endocrine and immune systems to deal with changing diet and the concentrated number of pathogens which develop around settlements.

This source introduces a new and inspirational theory on domestication based on subgenomics which have unusually high rates of mutation. The source also presented the retrotransposon: A genetic quirk which encourages abnormally high rates of mutation in specific sections of gene code. It answers the question of why certain species are better subjects for domestication; they have a greater affinity for genetic variability. This source is useful for anyone researching theories behind domestication or abnormalities in genetic code.

Grossen C, Keller L, Biebach I, Croll D (2014) Introgression from Domestic Goat Generated Variation at the Major Histocompatibility Complex of Alpine Ibex.PLoS Genet 10(6): e1004438. doi: 10.1371/journal.pgen.1004438

This source describes how the introgression of domesticated goat genes impacted the genetic and morphological structure of the Alpine Ibex. The major focus of the introgression's impact is on histocompatibility, the body's ability to interact with foreign substances, such as allergens and skin grafts. One might say it is the body's natural system of antihistamines. The Alpine Ibex was at one point on the brink of extinction, and, when reintroduced to many areas, the gene pools were quite small. In order to prevent potential genetic mutation which could to the specie's demise, a few domesticated goats were bred with the Ibex. This caused some purebred

Ibex genes to become a little muddied up. The only reason the Ibex have two alleles for histocompatability rather one, comparable to the innumerable quantity of alleles the domesticated goat has for this trait, is the interbreeding of the two species. Now many sick Ibexes may have goat organs transplanted inside of them, which are very strong due to human selection, but the cost of removing the Alpine Ibex from its natural genetic state is notable. Many times over has such a case occurred in which a domesticated species breeds with and alters a wild one.

This source supported the theory that genetic introgression has had a large impact not only going out of domestication, but also coming in. Genetic introgression plays a large role in the genetic diversity of a species. The article answered the question of how introgression can impact a species. This would be a valuable resource for anyone who might be interested in genetic introgression or the repopulation of endangered species.

Hai Xiang,  Early Holocene chicken domestication in northern ChinaPNAS 2014 111 (49) 17564-17569; published ahead of print November 24, 2014,doi:10.1073/pnas.1411882111

Chickens represent by far the most important poultry species, yet the number, locations, and timings of their domestication have remained controversial for more than a century. Here we report ancient mitochondrial DNA sequences from the earliest archaeological chicken bones from China, dating back to ∼10,000 B.P. The results clearly show that all investigated bones, including the oldest from the Nanzhuangtou site, are derived from the genus Gallus, rather than any other related genus, such as Phasianus. Our analyses also suggest that northern China represents one region of the earliest chicken domestication, possibly dating as early as 10,000 y B.P. Similar to the evidence from pig domestication, our results suggest that these early domesticated chickens contributed to the gene pool of modern chicken populations. Moreover, our results support the idea that multiple members of the genus Gallus, specifically Gallus gallus and Gallus sonneratiicontributed to the gene pool of the modern domestic chicken. The results provide further support for the growing evidence of an early mixed agricultural complex in northern China. This in turn supports the theory of the domestication theory.

Hare, B., Wobber, V., & Wrangham, R. (2011). The self-domestication hypothesis: Evolution of bonobo psychology is due to selection against aggression. Animal Behaviour, 573-585. Retrieved September, 2014, from http://evolutionaryanthropology.duke.edu/uploads/media_it ems/hare-et-al-2012-self-domestication.original.pdf

This source discusses how the general behavior of the Bonobo monkeys in Africa may have domesticated themselves, in a way similar to what some anthropologists believe humans

may have done. The theory is that the natural selection of the animals has been against aggression, due to the free availability of food, and that this same anti-aggressive trait is looked for during domestication, so these animals have domesticated themselves. Researchers looked for common changes in domesticated animals, both phenotypical and morphological traits; the Bonobos showed many promising changes that support this theory. Males and females treat one another more equally, mature specimens maintain juvenile traits, brains are smaller than there simian relatives, and they have reduced predatory behaviors; these traits are all practically universal in the domesticated mammal community. This idea of self domestication is on the cutting edge of both genetics and anthropology.

This source describes a new and valuable research endeavor that strives to determine if a species is able to domesticate itself. Any genetic or anthropological researcher could use this to support the theory that domestication is first influenced by behavior, not physical or morphological development; it is also an invaluable and pristine example of domestication in the works, uninfluenced by human interference. This research helps to answer the penultimate question of how an animal truly becomes domesticated, and not just tame.

Kadwell, M., Bruford, M., Fernandez, M., Stanley, H., Baldi, R., Wheeler, J., & Rosadio, R. (2001). Genetic Analysis Reveals The Wild Ancestors Of The Llama And The Alpaca. Proceedings: Biological Sciences, 268(1485), 2575-2584.

This source discusses how researchers found the ancestral origins of alpacas and llamas. At the beginning of the experiment, the Alpacas ancestor was thought to be the still living South American camelid known as the Vicuna while Llammas were thought to hail from the Guanaco of South America, a species which covers an even greater range along the Andes Mountains than the Vicuna. However, the researchers found some very interesting correlations. The Alpaca DNA correlated 25% to that of llamas, indicating some cross breeding with the species. This completely altered the genome of the Alpaca, making it quite different from that of the Vicuna. This inbreeding could have been accidental, or it could, more likely, have been to create a hardier breed, as llamas do quite well in the mountains. This would support the theory of morphological development because these animals were directly bred for their traits.

Knut H Røed Genetic analyses reveal independent domestication origins of Eurasian reindeer

Proc. R. Soc. B:2008275 1849-1855;DOI: 10.1098/rspb.2008.0332.Published 22 August 2008

Although there is little doubt that the domestication of mammals was instrumental for the modernization of human societies, even basic features of the path towards domestication remain largely unresolved for many species. Reindeer are considered to be in the early phase of domestication with wild and domestic herds still coexisting widely across Eurasia. This provides a unique model system for understanding how the early domestication process may have taken

place. We analysed mitochondrial sequences and nuclear microsatellites in domestic and wild herds throughout Eurasia to address the origin of reindeer herding and domestication history. Our data demonstrate independent origins of domestic reindeer in Russia and Fennoscandia. This implies that the Saami people of Fennoscandia domesticated their own reindeer independently of the indigenous cultures in western Russia. We also found that augmentation of local reindeer herds by crossing with wild animals has been common. However, some wild reindeer populations have not contributed to the domestic gene pool, suggesting variation in domestication potential among populations. These differences may explain why geographically isolated indigenous groups have been able to make the technological shift from mobile hunting to large-scale reindeer pastoralism independently.

MacHugh, D. (1997). Microsattelite DNA Variation and the Evolution, Domestication and Phylogeography of Taurine and Zebu Cattle (Bos tuum and Bos indicus). Genetics, 146(3), 1071-1085. Retrieved October 15, 2014, from Genetics.org.

This article delves into the genetic separation of European Taurine cattle from Asian Zebu cattle and both of those separating from the American Bison. There are significant differences in all of these bovine relatives, most visibly the hump on their back or the lack thereof. The researchers determined the genes of the Zebu and Taurine cattle split 210,000 years, denouncing the commonly shared idea that Zebu cattle evolved from the same subspecies of Aurochs as the Taurine cattle. They now believe the Zebu cattle came from a separate subspecies of Aurochs from southern Asia. The researchers discussed how the cattle were selectively bred for length of milk production after having a calf, as well as quality of meat. This supports the theory of morhphological domestication being foremost in the domestication process. It discusses, as several other articles have, the light or white coloration being a result of the pigments not being able to travel through the body on proteins. This supports the central concept of the domestication syndrome that the embryo does not spread its basic components as it should.

This source would be very useful to anyone researching domestication of bovines, or anyone researching the genetic development of a domesticated species. It makes the reader wonder when the American Buffalo left the equation. This source supports the theory that domestication is a primarily morphological occurrence.

McCue, M. (2012). A High Density SNP Array for the Domestic Horse and Extant Perissodactyla: Utility for Association Mapping, Genetic Diversity, and Phylogeny Studies. PLoS Genetics, 8(1), 1-14. Retrieved October 11, 2014, from PLOS Genetics.a

This source compared the genomes of several breeds of domesticated horses and their closest wild relatives. The study provided some unique and somewhat unexpected insights. The

domesticated horses were, as expected, more closely related to the zebras and przewalski's horses than the tapirs and rhinoceroses. Much of the genomic change found in the horses was however due to inbreeding, causing many genotypical and phenotypical changes in the various breeds. This introduced the question of just how much impact the domestication process had on these breeds. The inbreeding caused a great decrease in genetic diversity, which meant that many mutations occurred that otherwise would not. The researchers believed that this may have been because the original domesticators of these animals were only able to handle small numbers and therefore were inbreeding them because they bred only what they had. Researchers discovered this finding because there was a "linkage disequilibrium": an absence of correlation between the predicted amount of variation in the genome, and the actual amount of variation. In this case, the variation was much greater than expected, a common sign of inbreeding.

This source inspires the reader to consider a very important and seemingly overlooked question: Are the ancient domesticated animals structured morphologically and physically because of their domestication, or are they structured as such because of something else? This source could be used by those researching the impact of inbreeding on domesticated animals, or by those researching how domesticated animals have become what they are today.

Michael J. Montague, Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication PNAS 2014 111 (48) 17230-17235; published ahead of print November 10, 2014,doi:10.1073/pnas.1410083111

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.

Natt, D., Ruban, C., Wright, D., Johnsson, M., Belteky, J., Andersson, L., & Jensen, P. (2012).Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens (59th ed., Vol. 13). BioMed Central.

This article describes the development and change in the modern chicken from its ancestor, the Red Junglefowl. The modern chicken, in this case, the White Leghorn breed, displays a very different mindset than the Red Junglefowl; they show less fear, less stress, and more intelligence. The Red Junglefowl is also very physically different from the modern chicken; chickens are twice as large, and their eggs are too. They also lay them faster and sooner than the Junglefowl. The hypothalamus in the modern chicken functions quite differently from the hypothalamus of the Red Junglefowl, with "methylation" processes which measure function being far higher in the modern chicken than the Junglefowl. It is concluded with the determination that all of these morphological and mental changes are due to intensive selection during the domestication process. There is also some consideration that some of the behavioral changes may be for environmental reasons because domesticated animals are generally raised in more hospitable environments than others.

This article demonstrated the change that can occur in a species as it develops and becomes domesticated. This research informed the reader of how the mind of a domesticated animal differs from a wild one and how it changes physically as well; it also informed the reader of the methods one can use to study psychological change in animal. This article could be used for evidence that psychological change in domesticated animals is genetic, more so than environmental, and that interspecies domestication demonstrates similar trait expression.

Nelson, A. (2004). Development of the Domestic Donkey. Science, 305, 1781-1781.

This source discusses the genetic origins of the donkey, equus asinus. Donkeys are an interesting source of study because they are one of the few species not bred for the sustenance of people, but instead for their strength. The researchers found that the domestication of donkeys coincided with the rise of mass transportation, so the genes manipulated in breeding were primarily strength and endurance. The researchers found that the progenitors of the donkeys came from Africa, a bustling area at the time of domestication, and the link in variability between various domesticated species. The two progenitors were the Nubian wild ass from north central Africa and the Somali wild ass from northeastern Africa. Researchers also found that there were multiple separate incidences of the domestication of donkeys from already genetically different populations of asses. The greatest source of variation was in the MC15T gene, a gene related to nutrient digestion. This gene was likely changed because the different populations of donkeys, which developed in different parts of the world, eat different foods and need to digest there food differently.

O'Brien, S. (Director) (2013, October 16). The Cat: evolution, domestication and Genome 10k. Opening of the UDC Earth Institute. Lecture conducted from University Dublin College, Dublin.

The modern domesticated cat was domesticated in the Middle East approximately 9,500 years ago. Cats have a remarkably high level of homogeny, due to their self domestication as well as breeding in recent years. There domestication prevented development of inbred diseases because the cats domesticated themselves, essentially in another step of natural selection. This also allowed a buildup of resistance to other diseases, and also maintenance of an appearance relatively close to their ancestors, such as the sandcat. The cat is the best example currently in existence of an unmodified domesticated species. Only the basic changes of domestication occurred in the cat for the first 8,500 years until humans began breeding them for preferred traits. In a cat one can see the retainment of the juvenile traits in a domesticated cat’s face, the lengthening of its tail, and the unique coat colors. The cat’s interaction with disease is being compared to that have humans in order to advance medicine.

This source supports the idea of morphological development, as the cats physical traits all changed so they could specifically thrive better in their newly established environment around humans. The source would be useful for anyone wondering how cats developed and how they can help society today, or anyone wondering how the genome works. This source answers questions about how domesticated animals change from their ancestors and how certain species can domesticate themselves.

Ostrander, E. (2006). Orpohology and Behavior: Are They Coupled at the Genome Level? In The dog and its genome (pp. 82-93). Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press.

This chapter from the book The Dog and its Genome discusses the relationship and development of both domesticated foxes and dogs; they both have a distant ancestor in Canis Familias, or the common wolf, and so may be likened and compared more closely to one another. The measurements to determine changes were measured in five different groups of wolves: "Tame, aggressive, unselected, hybrid (tame x aggressive), and backcross (hybrid x tame)" along with the Portuguese Water Dog. They were measured for various physical and behavioral attributes, such as cranial circumference, ocular diameter, coccygeal length, calmness, willingness to interact, and shyness. These all showed similar results in both fully domesticated canines and the backcrosses except for ocular diameter; the diameter of the dogs tended to remain the same, whereas it contracted in the foxes, more so for the domesticated foxes than the backcrosses. The researchers believed this might correlate with research pertaining to pigs, but do not know why it occurred.

This chapter gives a thorough description of two different domesticated species, introduces new and significant vocabulary as well as valid and pertinent questions. This article provides bountiful evidence that domesticated animals vary significantly from their wild counterparts and shows how independent efforts of domestication exhibit quite similar results. It informs the reader in a precise and concise fashion how the domesticated dogs and foxes are similar and different. The information presented may be used to support the theory that separate incidents of domestication produce similar results.

P. Gepts, T.R. Famula, R.L. Bettinger 2012 Pathways to Animal Domestication. In Biodiversity . in Agriculture: Domestication, Evolution, and Sustainability, pp. 227-229. Cambridge . University Press, Cambridge

This source provides a theory that there are multiple ways for an animal to become domesticated. In every path, it is recognized that domestication is a process, not a spontaneous occurrence. Some theories support the idea that humans do most of the work domesticating, but many others disagree, stating that the animals do more work becoming domesticated, and others yet lend backing to the theory that domestication is a mutual relationship between the two. The journal also supports the idea that people domesticate based on behavioral aspects. The author states what she believes to be a set list of traits which are looked for in a species in candidacy for domestication. She says that an animal which will have less change in its domesticated habitat is more fit to be domesticated, and will be domesticated more quickly. Zeder believes the primary change in a domesticated animal is its reformed brain and its reduced size. The morphological and physical changes are the secondary factors, only afterthoughts of the taming of a species. She believes that the difference between a tame and domesticated animal is that a domesticated animal cannot truly turn back to its fore-generations' ways of life. She says feral animals cannot live the same way their wild counterparts do.

This source provided many new and intriguing theories about domestication. These theories can develop into a thesis. It is a valuable aid to the research question. This source would be quite useful to anyone curious about the various routes as to which an animal may become domesticated, as it explains this clearly and concisely.

Petersen, J. (2013). Genome-Wide Analysis Reveals Selection for Important Traits in Domestic Horse Breeds. PLOS Genetics, 9(1), 1-17. Retrieved October 2, 2014, from http://www.plosgenetics.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pgen.1003211&representation=PDF

This article examines the various branches of development in the ongoing act of equine domestication and how selection has shaped each of 33 different breeds. The first trait observed was coat color, influenced by the "MC1R gene." Some breeds, such as the Norwegian Warmblood, are bred specifically for coat color; they demonstrated quite uniform coding for MC1R. An interesting finding was that certain breeds demonstrated a higher chance for a unique, recessive mutation of the MC1R gene which causes Chestnut coloration to occur. Another interesting and uniquely equine form studied was the selective gait development in breeds such as the Tennessee Walking Horse, Standardbred, and Peruvian Paso. All of these breeds have unique gaits, and there genomes provide evidence that there are neural and morphological changes which support the development of these unnatural gaits. After studying the ECA23 region of the genome, thought to impact the gait, the researchers to the conclusion that there was in fact a commonly shared "haplotype" of identical length in each of the gaited breeds' genomes.

This source provided valuable evidence for the theory that selection and genetic development are the greatest impacts on how a domesticated species becomes what it is. Small variations in the genome can lead to both large physical and morphological phenotypical changes. This source would be valued by horse breeders and those researching the impact of selective breeding on a specie's genotype.

Sakudoh, T., Nakashima, T., Kuroki, Y., Fujiyama, A., Kohara, Y., Honda, N., ... Tsuchida, K. (2011). Diversity in Copy Number and Structure of a Silkworm Morphogenetic Gene as a Result of Domestication. Genetics, 187(3), 965-976. Retrieved October 15, 2014, from Genetics.org.

This article focuses on the silkworm: a species which does not always come to mind when one hears the word domestication but a domesticated species all the same. As silkworms have become increasingly domesticated, the protein they produce silk with, cartenoid binding protein (CBP), has been significantly changed, with the gene copy number sometimes reaching twenty. This caused a change in the coloration of the silk, and the silk is the whole reason this species was domesticated. Along with domestication, the researchers believe inbreeding has played in the color change of the silk. The colors can vary from white to yellow to pink and even to green; wild silkworms produce only yellow and green. A series of "hydrophobic pigments" of yellow color found in certain strains of CBP are thought to cause the yellow coloration. White threads in the domesticated species have researchers believing that there is an issue in genomic piggybacking on the protein, something very central to the idea of the domestication syndrome. The change in silk color was thought to be due to selective breeding by silk farmers trying to influence the time's fashion.

This article would be useful to any individual researching the development of the silk industry or the alteration of insects as they become domesticated. It inspires the question of what causes these colors specifically to develop, and not blue, purple, or orange. It provides great support for the domestication syndrome, with the inability of the pigments to piggyback on the proteins they would travel within the wild.

Sauvage, C., Derome, N., Normandeau, E., St.-Cyr, J., Audet, C., & Bernatchez, L. (2010). Fast Transcriptional Responses to Domestication in the Brook Charr Salvelinus fontinalis. Genetics, 185(1), 105-112. Retrieved September 26, 2014, from Genetics.org.

This source describes a study of a population Brook Charr, selectively bred over four generations, which provides evidence supporting the theory of the “domestication syndrome.” The Brook Charr showed substantially supportive changes in the cDNA, of which 32,000 different features were studied. Another interesting correlation was the similarities between this study of the Brook Charr over four generations, and a study of Atlantic Salmon studied over seven generation; the changes in these species have been all encompassing, but focusing on a select number of very important genes. These have changed the digestion of carbs and lipids, the strength of the immune system, and even how the subject’s cells themselves are formed. Subjects have also shown increased growth rates and slowed sexual maturation: traits selectively bred for. These selectively bred fish provide insight into an often overlooked area of domestication.

This study could be well used by a researcher or someone developing another study; it identifies a list of possible genes which could be looked for in an interspecies and perhaps interclass study. It provides evidence and support for the domestication theory, stating that the neural changes are the leading cause for the rest of the domesticated traits and that interspecies domestication demonstrates similar trait expression. This source also spreads light upon how other classes in the Animalia kingdom are affected by domestication and how they evolve similarly to other classes. It lends support to the Domestication theory overall.

Trut, L. (1999). Early Canid Domestication:The Farm-Fox Experiment. American Scientist, 87(2), 160- 169. Retrieved September 17, 2014, from http://155.97.32.9/~bbenham/2510 Spring 09/Behavior Genetics/Farm-Fox Experiment.pdf

This article gives a detailed overview of the Russian Silver Fox domestication experiment led by Dimitry Belyaev, and his marvelous theory of why domesticated animals become what they are. Belyaev used foxes from the Russian commercial fur industry because they were already used to being handled by people allowing the breeding process to accelerate and the domestication to occur faster. Belyaev's theory, based on his research, was that all things shared in domesticated animals were due not to the alteration of quantitative traits, as many previous theories claimed, but rather behavioral traits. He worked to prove this by breeding his

experimental group solely for tameness, and, after 30 years, his domesticated foxes fit the exact profile of other domesticated species. The selection process for tame animals in this experiment is quite deliberate and careful, with only the most tame of each generation being chosen for breeding in the next one. It was found that the period in which the animals did not fear new stimuli, in order to adapt to surroundings, was extended to almost twice as long, allowing them to better adjust to the humans they grow up alongside. An interesting trait that appeared, which is thought to change the reproduction cycle, was pedomorphosis: the maintenance of the foxes' juvenile traits as they mature. This is thought to make the animals sexually mature faster and make them able to reproduce more often.

This article provides a validly supported theory about what makes domesticated animals what they are. It provides an invaluable modern example of domestication, giving fresh evidence about what may cause it and allowing others to discover how it works. It informs the reader of additional, previously unknown traits that can be found in domesticated animals. This information can be used to verify the theory that domestication is based primarily on neural behavior and not upbringing in a certain environment.

Vila, C. (2001). Widespread Origins of Domestic Horse Lineages. Science, 291(5503), 474-477.

This source discusses the various lineages of domesticated horses and how they have come together genetically. As the most widely tamed creature on the planet, different breeds of horse have abnormally high levels of genetic variation when compared to one another. While some horses were bred for meat and milk with breeders focusing on internal development, others were developed into a form of transportation, so these animals did not even have the same genes altered. The source establishes a hypothesis that the divergence of horses did not occur at domestication, with different groups mutating and being bred separately, but still originating from one population of horses; rather, it states that the domestication of horses occurred on several different occasions in separate parts of the world from separate, already genetically diverse populations of horses. Researchers found six separate clades which, based on the degree genetic variation, had to begin hundreds of thousands of years before the initial domestication of horses occurred. The researchers also found an intriguing piece of information relating to the Prezwalski’s horse that contradicted there other findings. The Prezwalski’s had shockingly low levels of variation when compared to modern horses, and they are the closest living example of the domesticated horse’s ancestors, so they should not be so closely related, based on all of the other findings in the study.

This source supports the idea of the morphological development, because these creatures were selected specifically for their given traits. This therefore caused the change in the DNA sequencing. This source answers the question of how the modern horse has come to be what it is, but also introduces the question of why they differ so little from their closest living ancestor. The source is valuable to anyone researching equine origins or domestication.

Wang, Z., Yonezawa, T., Liu, B., Ma, T., Shen, X., Su, J., ... Liu, J. (2010). Domestication Relaxed Selective Constraints on the Yak Mitochondrial Genome. Molecular Biology and Evolution,28(5), 1553-1556. Retrieved December 18, 2014, from http://mbe.oxfordjournals.org/content/28/5/1553.abstract

This source studies a certain area of the yak genome in order to see how domestication has influenced and altered it. Mitochondria are the powerhouses, the generators of energy, in any life form. Every living cell on this planet and those up in the space stations too, contain mitochondria. The wild yaks live in extremely high, extremely cold, extremely barren altitudes. This lifestyle has caused their mitochondria to adapt in order to maintain quite a high level of efficiency for the little they get to work within the yaks diet. This makes the yaks leanness, a prized quality in meat, a nonissue for its survival, because it runs just as well as a normal bovine relative on a smaller number of calories. The mitochondria’s ability did not change because of human intentions, but because of the yak’s requirement for more efficient energy production in order to survive. This is evidence which supports the idea of the domestication syndrome.

Wilkins, A., Wrangham, R., & Fitch, W. (2014). The “Domestication Syndrome” Mammals: A ` Unified Explanation Based on Neural Crest Cell Behavior and Genetics. Genetics Society of ` America, 197(3). Retrieved September 10, 2014, from: . http://www.genetics.org/content/197/3/795.full

This article synthesizes a new idea about how the phenotypical changes occur in domesticated subjects; “neural crest cells” are developed during the embryonic stage and are supposed to travel all throughout the animal during this stage. These cells often fail to migrate in domesticated subjects, causing certain genetic switches not to turn on, altering multiple different attributes: behavior, intelligence, sociability, and appearance. When “neural crest cells” successfully complete their migration, they activate these switches, causing brain growth, pigmentation, cartilage development, and many other embryonic changes. The patterns of failed migrations of the cells are found to repeat to some degree throughout all domesticated mammals; however, it is also believed that, to some degree, the raising of the mammal in a safe, nurturing environment influences its friendly behavior toward people. The primary study subjects for these findings were German rats and Russian silver foxes; while rats provided quicker results, the findings with the foxes were more applicable to large mammals, which are more commonly domesticated than small mammals.

This article provided a direct argument as to why domesticated animals look and behave the way they do. It introduced new concepts and conveyed new ideas from the synthesis and evaluation of other studies in a comprehensible fashion; all of the basic points of change in domesticated animals were well covered and explained. It introduced the theory of the

domestication syndrome. It was useful for someone researching various theories about what makes a domesticated mammal what it is.