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Part II
ARTIFICIAL SELECTION, OR ADAPTATION TO HUMAN DEMANDS

Darwin titled the first chapter in The Origin of Species “variation under domestication,” probably because he felt that developing a case for the effectiveness of human-mediated selection in generating new domestic varieties would facilitate his efforts in later chapters to communicate the concept of how natural selection can generate new varieties and species in nature. In chapter 1 of The Origin, Darwin discussed several domesticated plant and animal species, ranging from beans, melons, and plums to dogs, cattle, and horses. He devoted a long section to how selective breeding had altered the domestic pigeon, fancy varieties of which were widely prized in the Victorian era. Nearly 10 years later, he would expand greatly on these themes in The Variation of Animals and Plants Under Domestication.

In chapter 1 of The Origin, Darwin lamented that “We hardly know anything about the origin or history of our domestic breeds”; and “The origin of most of our domestic animals will probably for ever remain vague.” Darwin would therefore be both pleased and surprised by recent scientific progress in deciphering the evolutionary origins of many domesticated plant and animal species. Much of this evidence has come from molecular genetic and phylogenetic analyses of domesticated breeds vis-à-vis their wild ancestors. Carlos Driscoll, David Macdonald, and Steve O’Brien tabulate some of this evidence in Chapter 5, for various domestic animals, and then provide a detailed case in point by describing the phylogenetic and biological history of the domestic cat. The cat appears to be nearly unique among animal domesticates (including dogs) in the sense that it



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Part II ARTIFICIAL SELECTION, OR ADAPTATION TO HUMAN DEMANDS D arwin titled the first chapter in The Origin of Species “variation under domestication,” probably because he felt that develop- ing a case for the effectiveness of human-mediated selection in generating new domestic varieties would facilitate his efforts in later chapters to communicate the concept of how natural selection can gener- ate new varieties and species in nature. in chapter 1 of The Origin, Darwin discussed several domesticated plant and animal species, ranging from beans, melons, and plums to dogs, cattle, and horses. he devoted a long section to how selective breeding had altered the domestic pigeon, fancy varieties of which were widely prized in the victorian era. nearly 10 years later, he would expand greatly on these themes in The Variation of Animals and Plants Under Domestication. in chapter 1 of The Origin, Darwin lamented that “We hardly know anything about the origin or history of our domestic breeds”; and “The ori- gin of most of our domestic animals will probably for ever remain vague.” Darwin would therefore be both pleased and surprised by recent scientific progress in deciphering the evolutionary origins of many domesticated plant and animal species. Much of this evidence has come from molecular genetic and phylogenetic analyses of domesticated breeds vis-à-vis their wild ancestors. Carlos Driscoll, David Macdonald, and steve o’Brien tabulate some of this evidence in Chapter 5, for various domestic animals, and then provide a detailed case in point by describing the phylogenetic and biological history of the domestic cat. The cat appears to be nearly unique among animal domesticates (including dogs) in the sense that it 

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 / Part II was initially self-selected for tolerance to humans, rather than actively selected by humans for tameness or for desired services such as com- panionship, hunting or guard duties, or food. According to the authors’ reconstruction, cat domestication probably began near some of the earliest agricultural settlements of the neolithic, in the Fertile Crescent region of the near east, as wildcats became accustomed to feeding on rodents and refuse near human towns. if so, their evolution to companion animals, and their ecological isolation from wildcats, was initially a response to natural selection more so than to conscious artificial selection. Apart from appraising the phylogenetic histories of domestic organ- isms, the field of molecular genetics is also uncovering the genes respon- sible for key phenotypes that have emerged from artificial selection. in Chapter 6, Feng Tian, natalie stevens, and edward Buckler iv provide cases in point involving domestic corn (maize), the ancestors of which are wild teosinte grasses native to Mexico. The evolutionary transformation from teosinte to maize ranks among the most impressive of all feats of artificial selection. For example, teosinte lacks a cob-like inflorescence and instead produces only 6–12 kernels in two rows protected by a hard cover- ing, whereas each cob of modern maize consists of approximately 20 rows with numerous exposed kernels; and teosinte has long lateral branches ter- minated by male tassels, whereas modern maize has short lateral branches tipped by female ears. The authors review current knowledge about the genetic loci responsible for these and other such morphological transi- tions. several genes with major effect can be specified, and many others are implicated, including a newly discovered region on chromosome 10 that spans more than 1,000,000 base pairs and retains the molecular footprints of strong artificial selection during the domestication process. in Chapter 7, Fred Allendorf and Jeffrey hard describe another form of human-induced selection that they term unnatural selection. When breed- ers artificially select domestic animals for food or companionship, they purposefully try to propagate traits that people deem desirable. however, hunting and fishing (especially for trophies) routinely violate such ground rules by culling rather than propagating the animals that humans prize most. in other words, unnatural selection via hunting, unlike artificial selection by people (or natural selection by nature), often eventuates biotic outcomes that run counter to what humans (or nature) otherwise would strive to achieve. For example, the evolutionary responses to the contin- ued selective removal of larger or healthier animals from a population of deer or fish could include, in principle, earlier sexual maturation and smaller adult body sizes. The authors review arguments and empirical evi- dence for unnatural selection imposed by human harvests of wild animal populations, and they discuss the management problems generated by such selective mortality. Darwin mostly overlooked this important topic,

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Artificial Selection, or Adaptation to Human Demands /  which continues to be neglected by many wildlife and fishery agencies today. This paper may help to rectify that situation by bringing to broader attention the important contrasts between standard hunting and fishing practices (unnatural selection) on the one hand and standard agricultural and aquacultural practices (artificial selection) on the other. Artificial selection traditionally refers to human-mediated differential propagation of plants or animals with desirable hereditary traits. in the modern biotechnology era, an entirely different form of genetic engineer- ing is possible in which particular proteins are subjected to repeated rounds of mutation and selection, in laboratory test tubes, for improved stability or biochemical function. in Chapter 8, Jesse Bloom and Frances Arnold review this form of directed evolution, which is becoming a pow- erful approach to the design of new proteins for medicine and pharmacol- ogy. Directed protein evolution has also yielded new insights into the fun- damental nature of evolutionary processes. The authors emphasize three major conclusions from directed evolution experiments: (i) most desirable protein properties can be incrementally improved through successions of single mutation steps; (ii) much of the epistatic coupling between muta- tions is due to protein stability and its influence on mutational robustness and protein evolvability; and (iii) adaptive protein evolution is heavily reliant on the prevalence of promiscuous protein functions (initial traces of activity that proteins routinely display on foreign substrates) that in turn are routinely influenced by neutral mutations. Directed protein evolution goes far beyond the wildest imaginings of Darwin, who would doubtless be impressed that the general principles of selection he illuminated would prove to be so universal.

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