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Thogerson", + "page": 0, + "order": 2, + "type": "content" + }, + { + "text": "Greg A. Vicino", + "page": 0, + "order": 3, + "type": "content" + }, + { + "text": "1", + "page": 0, + "order": 4, + "type": "content" + }, + { + "text": " Ecological Services, U.S. Fish & Wildlife Service, Arlington, Virginia, United States of America,", + "page": 0, + "order": 5, + "type": "content" + }, + { + "text": "Indiana, United States of America,", + "page": 0, + "order": 6, + "type": "content" + }, + { + "text": "Poultry Science, University of Guelph, Ontario, Canada,", + "page": 0, + "order": 7, + "type": "content" + }, + { + "text": "Global, San Diego, California, United States of America,", + "page": 0, + "order": 8, + "type": "content" + }, + { + "text": "Stanford University, Stanford, California, United States of America ", + "page": 0, + "order": 9, + "type": "content" + }, + { + "text": "Abstract ", + "page": 0, + "order": 10, + "type": "content" + }, + { + "text": "Population dynamics predicts that on average parents should invest equally in male and female offspring; similarly, the ", + "page": 0, + "order": 11, + "type": "content" + }, + { + "text": "physiology of mammalian sex determination is supposedly stochastic, producing equal numbers of sons and daughters. ", + "page": 0, + "order": 12, + "type": "content" + }, + { + "text": "However, a high quality parent can maximize fitness by biasing their birth sex ratio (SR) to the sex with the greatest ", + "page": 0, + "order": 13, + "type": "content" + }, + { + "text": "potential to disproportionately outperform peers. All SR manipulation theories share a fundamental prediction: ", + "page": 0, + "order": 14, + "type": "content" + }, + { + "text": "grandparents who bias birth SR should produce more grandoffspring via the favored sex. The celebrated examples of ", + "page": 0, + "order": 15, + "type": "content" + }, + { + "text": "biased birth SRs in nature consistent with SR manipulation theories provide compelling circumstantial evidence. However, ", + "page": 0, + "order": 16, + "type": "content" + }, + { + "text": "this prediction has never been directly tested in mammals, primarily because the complete three-generation pedigrees ", + "page": 0, + "order": 17, + "type": "content" + }, + { + "text": "needed to test whether individual favored offspring produce more grandoffspring for the biasing grandparent are ", + "page": 0, + "order": 18, + "type": "content" + }, + { + "text": "essentially impossible to obtain in nature. Three-generation pedigrees were constructed using 90 years of captive breeding ", + "page": 0, + "order": 19, + "type": "content" + }, + { + "text": "records from 198 mammalian species. Male and female grandparents consistently biased their birth SR toward the sex that ", + "page": 0, + "order": 20, + "type": "content" + }, + { + "text": "maximized second-generation success. The most strongly male-biased granddams and grandsires produced respectively ", + "page": 0, + "order": 21, + "type": "content" + }, + { + "text": "29% and 25% more grandoffspring than non-skewing conspecifics. The sons of the most male-biasing granddams were 2.7 ", + "page": 0, + "order": 22, + "type": "content" + }, + { + "text": "times as fecund as those of granddams with a 50:50 bias (similar results are seen in grandsires). Daughters of the strongest ", + "page": 0, + "order": 23, + "type": "content" + }, + { + "text": "female-biasing granddams were 1.2 times as fecund as those of non-biasing females (this effect is not seen in grandsires). To ", + "page": 0, + "order": 24, + "type": "content" + }, + { + "text": "our knowledge, these results are the first formal test of the hypothesis that birth SR manipulation is adaptive in mammals in ", + "page": 0, + "order": 25, + "type": "content" + }, + { + "text": "terms of grandchildren produced, showing that SR manipulation can explain biased birth SR in general across mammalian ", + "page": 0, + "order": 26, + "type": "content" + }, + { + "text": "species. These findings also have practical implications: parental control of birth SR has the potential to accelerate genetic ", + "page": 0, + "order": 27, + "type": "content" + }, + { + "text": "loss and risk of extinction within captive populations of endangered species. ", + "page": 0, + "order": 28, + "type": "content" + }, + { + "text": "Citation:", + "page": 0, + "order": 29, + "type": "content" + }, + { + "text": "Grandchildren. PLoS ONE 8(7): e67867. doi:10.1371/journal.pone.0067867 ", + "page": 0, + "order": 30, + "type": "content" + }, + { + "text": "Editor:", + "page": 0, + "order": 31, + "type": "content" + }, + { + "text": "Received", + "page": 0, + "order": 32, + "type": "content" + }, + { + "text": "Copyright:", + "page": 0, + "order": 33, + "type": "content" + }, + { + "text": "unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ", + "page": 0, + "order": 34, + "type": "content" + }, + { + "text": "Funding:", + "page": 0, + "order": 35, + "type": "content" + }, + { + "text": "decision to publish, or preparation of the manuscript. ", + "page": 0, + "order": 36, + "type": "content" + }, + { + "text": "Competing Interests:", + "page": 0, + "order": 37, + "type": "content" + }, + { + "text": "study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors have declared that no competing interests exist. ", + "page": 0, + "order": 38, + "type": "content" + }, + { + "text": "* E-mail: jgarner@stanford.edu ", + "page": 0, + "order": 39, + "type": "content" + }, + { + "text": "Introduction ", + "page": 0, + "order": 40, + "type": "content" + }, + { + "text": "Sex ratio (SR) manipulation theory is one of the founding pillars ", + "page": 0, + "order": 41, + "type": "content" + }, + { + "text": "of sociobiology and modern evolutionary theory [1\u20133]. Early work ", + "page": 0, + "order": 42, + "type": "content" + }, + { + "text": "on ", + "page": 0, + "order": 43, + "type": "content" + }, + { + "text": "frequency-dependent ", + "page": 0, + "order": 44, + "type": "content" + }, + { + "text": "population dynamics (notably Fisher [1]) is celebrated for showing ", + "page": 0, + "order": 45, + "type": "content" + }, + { + "text": "that advantages to individual parents will lead to equal investment, ", + "page": 0, + "order": 46, + "type": "content" + }, + { + "text": "and stabilize the birth population sex ratio at 50:50. Sex allocation ", + "page": 0, + "order": 47, + "type": "content" + }, + { + "text": "theory, first proposed by Hamilton [2], builds on and also ", + "page": 0, + "order": 48, + "type": "content" + }, + { + "text": "challenges this work. If offspring sex can be manipulated, and a ", + "page": 0, + "order": 49, + "type": "content" + }, + { + "text": "grandparent can predict the likely success of their offspring, then a ", + "page": 0, + "order": 50, + "type": "content" + }, + { + "text": "grandparent ", + "page": 0, + "order": 51, + "type": "content" + }, + { + "text": "grandchildren produced) by biasing its birth sex ratio (SR) in ", + "page": 0, + "order": 52, + "type": "content" + }, + { + "text": "favor of the sex with the greatest potential to disproportionately ", + "page": 0, + "order": 53, + "type": "content" + }, + { + "text": "outperform ", + "page": 0, + "order": 54, + "type": "content" + }, + { + "text": "fitness, or fail to compete the least [2]. The physiology of ", + "page": 0, + "order": 55, + "type": "content" + }, + { + "text": "mammalian sex determination is supposedly stochastic, producing ", + "page": 0, + "order": 56, + "type": "content" + }, + { + "text": "PLOS ONE | www.plosone.org ", + "page": 0, + "order": 57, + "type": "content" + }, + { + "text": " Thogerson CM, Brady CM, Howard RD, Mason GJ, Pajor EA, et al. (2013) Winning the Genetic Lottery: Biasing Birth Sex Ratio Results in More ", + "page": 0, + "order": 58, + "type": "content" + }, + { + "text": " Samuli Helle, University of Turku, Finland ", + "page": 0, + "order": 59, + "type": "content" + }, + { + "text": " January 14, 2013;", + "page": 0, + "order": 60, + "type": "content" + }, + { + "text": " \ufffd", + "page": 0, + "order": 61, + "type": "content" + }, + { + "text": " 2013 Thogerson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits ", + "page": 0, + "order": 62, + "type": "content" + }, + { + "text": " The project was supported by a graduate stipend to CMT from Purdue University. The funders had no role in study design, data collection and analysis, ", + "page": 0, + "order": 63, + "type": "content" + }, + { + "text": "can ", + "page": 0, + "order": 64, + "type": "content" + }, + { + "text": "peers, ", + "page": 0, + "order": 65, + "type": "content" + }, + { + "text": "1", + "page": 0, + "order": 66, + "type": "content" + }, + { + "text": ", Colleen M. Brady", + "page": 0, + "order": 67, + "type": "content" + }, + { + "text": "6", + "page": 0, + "order": 68, + "type": "content" + }, + { + "text": ", Joseph P. Garner", + "page": 0, + "order": 69, + "type": "content" + }, + { + "text": " 3", + "page": 0, + "order": 70, + "type": "content" + }, + { + "text": " Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America,", + "page": 0, + "order": 71, + "type": "content" + }, + { + "text": " Accepted", + "page": 0, + "order": 72, + "type": "content" + }, + { + "text": " The authors have read the journal\u2019s policy declare that GAV has the following conflicts: GAV is employed by SDZG. SDZG had no role in ", + "page": 0, + "order": 73, + "type": "content" + }, + { + "text": "selection ", + "page": 0, + "order": 74, + "type": "content" + }, + { + "text": "obtain ", + "page": 0, + "order": 75, + "type": "content" + }, + { + "text": "a ", + "page": 0, + "order": 76, + "type": "content" + }, + { + "text": "fitness ", + "page": 0, + "order": 77, + "type": "content" + }, + { + "text": "disproportionately ", + "page": 0, + "order": 78, + "type": "content" + }, + { + "text": "7", + "page": 0, + "order": 79, + "type": "content" + }, + { + "text": " 5", + "page": 0, + "order": 80, + "type": "content" + }, + { + "text": " 7", + "page": 0, + "order": 81, + "type": "content" + }, + { + "text": " May 21, 2013;", + "page": 0, + "order": 82, + "type": "content" + }, + { + "text": "on ", + "page": 0, + "order": 83, + "type": "content" + }, + { + "text": "gender ", + "page": 0, + "order": 84, + "type": "content" + }, + { + "text": "advantage ", + "page": 0, + "order": 85, + "type": "content" + }, + { + "text": "contribute ", + "page": 0, + "order": 86, + "type": "content" + }, + { + "text": "2", + "page": 0, + "order": 87, + "type": "content" + }, + { + "text": ", Richard D. Howard", + "page": 0, + "order": 88, + "type": "content" + }, + { + "text": "* ", + "page": 0, + "order": 89, + "type": "content" + }, + { + "text": " Veterinary Medicine, University of Calgary, Alberta, Canada,", + "page": 0, + "order": 90, + "type": "content" + }, + { + "text": " Department of Comparative Medicine, and by Courtesy, Department of Psychiatry and Behavioral Sciences, ", + "page": 0, + "order": 91, + "type": "content" + }, + { + "text": " Published", + "page": 0, + "order": 92, + "type": "content" + }, + { + "text": " July 10, 2013 ", + "page": 0, + "order": 93, + "type": "content" + }, + { + "text": "and ", + "page": 0, + "order": 94, + "type": "content" + }, + { + "text": "resulting ", + "page": 0, + "order": 95, + "type": "content" + }, + { + "text": "(in ", + "page": 0, + "order": 96, + "type": "content" + }, + { + "text": "terms ", + "page": 0, + "order": 97, + "type": "content" + }, + { + "text": "to ", + "page": 0, + "order": 98, + "type": "content" + }, + { + "text": "inclusive ", + "page": 0, + "order": 99, + "type": "content" + }, + { + "text": "equal numbers of sons and daughters. Nevertheless if functional ", + "page": 0, + "order": 100, + "type": "content" + }, + { + "text": "consequences of SR manipulation were to be found in mammals, ", + "page": 0, + "order": 101, + "type": "content" + }, + { + "text": "then it would suggest that mammals (either in individual species, ", + "page": 0, + "order": 102, + "type": "content" + }, + { + "text": "or in general), possess unknown physiological mechanisms to ", + "page": 0, + "order": 103, + "type": "content" + }, + { + "text": "control birth SR. Such a bridge between evolutionary and basic ", + "page": 0, + "order": 104, + "type": "content" + }, + { + "text": "molecular biology would be one of the most exciting implications ", + "page": 0, + "order": 105, + "type": "content" + }, + { + "text": "of SR manipulation (e.g. [4]). ", + "page": 0, + "order": 106, + "type": "content" + }, + { + "text": "Hamilton [2], focused on scenarios specific to particular insect ", + "page": 0, + "order": 107, + "type": "content" + }, + { + "text": "groups. In Mammals and birds a more general principle applies: ", + "page": 0, + "order": 108, + "type": "content" + }, + { + "text": "the number of offspring a male produces is often limited by how ", + "page": 0, + "order": 109, + "type": "content" + }, + { + "text": "many females he can mate with, while a female is limited by how ", + "page": 0, + "order": 110, + "type": "content" + }, + { + "text": "of ", + "page": 0, + "order": 111, + "type": "content" + }, + { + "text": "many ", + "page": 0, + "order": 112, + "type": "content" + }, + { + "text": "generates a tendency for males to vary more in first-generation ", + "page": 0, + "order": 113, + "type": "content" + }, + { + "text": "success than females. Thus male offspring are a high-risk-high- ", + "page": 0, + "order": 114, + "type": "content" + }, + { + "text": "reward bet for potential grandparents in the genetic lottery; while ", + "page": 0, + "order": 115, + "type": "content" + }, + { + "text": "females are a safe, hedged bet [5,6]. However, just like in insects, if ", + "page": 0, + "order": 116, + "type": "content" + }, + { + "text": "a grandparent \u2018knows\u2019 that a male offspring is a low-risk-high- ", + "page": 0, + "order": 117, + "type": "content" + }, + { + "text": "1 ", + "page": 0, + "order": 118, + "type": "content" + }, + { + "text": "3", + "page": 0, + "order": 119, + "type": "content" + }, + { + "text": ", Georgia J. Mason", + "page": 0, + "order": 120, + "type": "content" + }, + { + "text": " 2", + "page": 0, + "order": 121, + "type": "content" + }, + { + "text": " Department of Animal Sciences, Purdue University, West Lafayette, ", + "page": 0, + "order": 122, + "type": "content" + }, + { + "text": "offspring ", + "page": 0, + "order": 123, + "type": "content" + }, + { + "text": " 6", + "page": 0, + "order": 124, + "type": "content" + }, + { + "text": " Collections Husbandry Science, San Diego Zoo ", + "page": 0, + "order": 125, + "type": "content" + }, + { + "text": "she ", + "page": 0, + "order": 126, + "type": "content" + }, + { + "text": "can ", + "page": 0, + "order": 127, + "type": "content" + }, + { + "text": "physiologically ", + "page": 0, + "order": 128, + "type": "content" + }, + { + "text": "July 2013 | Volume 8 | Issue 7 | e67867 ", + "page": 0, + "order": 129, + "type": "content" + }, + { + "text": "4", + "page": 0, + "order": 130, + "type": "content" + }, + { + "text": ", Edmond A. Pajor", + "page": 0, + "order": 131, + "type": "content" + }, + { + "text": " 4", + "page": 0, + "order": 132, + "type": "content" + }, + { + "text": " Department of Animal and ", + "page": 0, + "order": 133, + "type": "content" + }, + { + "text": "produce ", + "page": 0, + "order": 134, + "type": "content" + }, + { + "text": "[5,6].This ", + "page": 0, + "order": 135, + "type": "content" + }, + { + "text": "5", + "page": 0, + "order": 136, + "type": "content" + }, + { + "text": ", ", + "page": 0, + "order": 137, + "type": "content" + }, + { + "text": "reward bet, then they can beat the house, and hit a jackpot (in ", + "page": 1, + "order": 0, + "type": "content" + }, + { + "text": "terms of grandchildren produced) [5,6]. Furthermore, grandpar- ", + "page": 1, + "order": 1, + "type": "content" + }, + { + "text": "ents can beat the house in other more subtle ways, leading later ", + "page": 1, + "order": 2, + "type": "content" + }, + { + "text": "authors to propose a variety of advantages to SR manipulation ", + "page": 1, + "order": 3, + "type": "content" + }, + { + "text": "that might apply to vertebrate species (e.g. local resource ", + "page": 1, + "order": 4, + "type": "content" + }, + { + "text": "competition or enhancement [3]). Each of these different SR ", + "page": 1, + "order": 5, + "type": "content" + }, + { + "text": "manipulation theories proposes different corresponding cues that ", + "page": 1, + "order": 6, + "type": "content" + }, + { + "text": "grandparents might use to predict the success of their offspring, ", + "page": 1, + "order": 7, + "type": "content" + }, + { + "text": "and corresponding selective pressures underlying these benefits (for ", + "page": 1, + "order": 8, + "type": "content" + }, + { + "text": "an excellent review, see [3]). For example (and most obviously), ", + "page": 1, + "order": 9, + "type": "content" + }, + { + "text": "parents can produce more of the sex most likely to out-reproduce ", + "page": 1, + "order": 10, + "type": "content" + }, + { + "text": "peers [2]; and either grandparent\u2019s quality or social status may be ", + "page": 1, + "order": 11, + "type": "content" + }, + { + "text": "excellent cues for the subsequent reproductive success of their ", + "page": 1, + "order": 12, + "type": "content" + }, + { + "text": "offspring relative to their potential competitors [5,6]. Thus high ", + "page": 1, + "order": 13, + "type": "content" + }, + { + "text": "quality granddams may bias towards males. Conversely, a low ", + "page": 1, + "order": 14, + "type": "content" + }, + { + "text": "quality or stressed granddam, may bias towards daughters, not ", + "page": 1, + "order": 15, + "type": "content" + }, + { + "text": "because they will outcompete peers, but because their failure to ", + "page": 1, + "order": 16, + "type": "content" + }, + { + "text": "compete will be less impactful than that of a son. Although this ", + "page": 1, + "order": 17, + "type": "content" + }, + { + "text": "example (the \u2018\u2018Trivers-Willard Hypothesis\u2019\u2019) is the most famous, ", + "page": 1, + "order": 18, + "type": "content" + }, + { + "text": "other benefits clearly occur through biasing towards the sex which ", + "page": 1, + "order": 19, + "type": "content" + }, + { + "text": "can reduce reproductive costs or competition, or maximize ", + "page": 1, + "order": 20, + "type": "content" + }, + { + "text": "inclusive fitness (for instance via enhanced production of the sex ", + "page": 1, + "order": 21, + "type": "content" + }, + { + "text": "that disperses; or the sex that provides care for younger siblings, ", + "page": 1, + "order": 22, + "type": "content" + }, + { + "text": "respectively [7]). Similarly, simple sexual selection can drive bias \u2013 ", + "page": 1, + "order": 23, + "type": "content" + }, + { + "text": "for instance, a granddam should bias towards males if the ", + "page": 1, + "order": 24, + "type": "content" + }, + { + "text": "grandsire excels in a sexually selected heritable trait that will result ", + "page": 1, + "order": 25, + "type": "content" + }, + { + "text": "in \u2018sexy sons\u2019, enhanced sperm competition, or other reproductive ", + "page": 1, + "order": 26, + "type": "content" + }, + { + "text": "advantages distinct from the maternal quality emphasized by the ", + "page": 1, + "order": 27, + "type": "content" + }, + { + "text": "Trivers-Willard Hypothesis. In nature, mammalian parents often ", + "page": 1, + "order": 28, + "type": "content" + }, + { + "text": "do bias birth SR in correlation with physiological, behavioral, or ", + "page": 1, + "order": 29, + "type": "content" + }, + { + "text": "environmental cues that are in turn consistent with these ideas (e.g. ", + "page": 1, + "order": 30, + "type": "content" + }, + { + "text": "[8\u201310]). For instance, dominant red deer mothers skew their SRs ", + "page": 1, + "order": 31, + "type": "content" + }, + { + "text": "toward sons, which is tantalizing as red deer stags with greater ", + "page": 1, + "order": 32, + "type": "content" + }, + { + "text": "mating success tend to have mothers of higher dominance [6]. ", + "page": 1, + "order": 33, + "type": "content" + }, + { + "text": "However, while this and other examples suggest that SR ", + "page": 1, + "order": 34, + "type": "content" + }, + { + "text": "manipulation could be adaptive, and are often taken as evidence of ", + "page": 1, + "order": 35, + "type": "content" + }, + { + "text": "such, they in fact provide only circumstantial evidence [3]. This ", + "page": 1, + "order": 36, + "type": "content" + }, + { + "text": "example, and all other mammalian studies to our knowledge, ", + "page": 1, + "order": 37, + "type": "content" + }, + { + "text": "require a leap of faith \u2013 the true test is to demonstrate that ", + "page": 1, + "order": 38, + "type": "content" + }, + { + "text": "grandparents with skewed birth SRs produce more grandchildren ", + "page": 1, + "order": 39, + "type": "content" + }, + { + "text": "than their peers [3], and that this benefit accrues specifically ", + "page": 1, + "order": 40, + "type": "content" + }, + { + "text": "through the biased individuals in the intermediate generation. In ", + "page": 1, + "order": 41, + "type": "content" + }, + { + "text": "other words, if a grandmother biases towards sons (for example), ", + "page": 1, + "order": 42, + "type": "content" + }, + { + "text": "then those particular sons must outcompete other males in their ", + "page": 1, + "order": 43, + "type": "content" + }, + { + "text": "generation to produce her more grandchildren in total, and more ", + "page": 1, + "order": 44, + "type": "content" + }, + { + "text": "grandchildren per son. Thus all SR manipulation theories (from ", + "page": 1, + "order": 45, + "type": "content" + }, + { + "text": "Trivers-Willard, to sexy sons, to local resource competition or ", + "page": 1, + "order": 46, + "type": "content" + }, + { + "text": "enhancement) all ultimately make the same prediction: that ", + "page": 1, + "order": 47, + "type": "content" + }, + { + "text": "favoring the sex with the greatest potential to disproportionately ", + "page": 1, + "order": 48, + "type": "content" + }, + { + "text": "outperform ", + "page": 1, + "order": 49, + "type": "content" + }, + { + "text": "fitness, or fail to compete the least, will mean that biased F1 ", + "page": 1, + "order": 50, + "type": "content" + }, + { + "text": "individuals should produce more F2 offspring", + "page": 1, + "order": 51, + "type": "content" + }, + { + "text": "non-biased peers. The power of this prediction is that it is agnostic ", + "page": 1, + "order": 52, + "type": "content" + }, + { + "text": "to the particular theory under test, the particular cues grandpar- ", + "page": 1, + "order": 53, + "type": "content" + }, + { + "text": "ents may be responding to, or the direction of bias; and hence ", + "page": 1, + "order": 54, + "type": "content" + }, + { + "text": "should be general across mammals irrespective of mating systems, ", + "page": 1, + "order": 55, + "type": "content" + }, + { + "text": "natural history, or their particular responses to captivity. However, ", + "page": 1, + "order": 56, + "type": "content" + }, + { + "text": "it has an Achilles\u2019 heel \u2013 testing it requires a complete three- ", + "page": 1, + "order": 57, + "type": "content" + }, + { + "text": "generation pedigree where every grandchild of every grandparent ", + "page": 1, + "order": 58, + "type": "content" + }, + { + "text": "is known [3,11], which is practically unobtainable in the wild. ", + "page": 1, + "order": 59, + "type": "content" + }, + { + "text": "Thus Clutton-Brock\u2019s seminal work in red deer [6] could not test ", + "page": 1, + "order": 60, + "type": "content" + }, + { + "text": "whether the females that produced more sons actually gained ", + "page": 1, + "order": 61, + "type": "content" + }, + { + "text": "more grandchildren; nor whether the successful sons descended ", + "page": 1, + "order": 62, + "type": "content" + }, + { + "text": "from the particular females who biased (because not all the ", + "page": 1, + "order": 63, + "type": "content" + }, + { + "text": "PLOS ONE | www.plosone.org ", + "page": 1, + "order": 64, + "type": "content" + }, + { + "text": "peers, ", + "page": 1, + "order": 65, + "type": "content" + }, + { + "text": "disproportionately ", + "page": 1, + "order": 66, + "type": "content" + }, + { + "text": "contribute ", + "page": 1, + "order": 67, + "type": "content" + }, + { + "text": " per capita", + "page": 1, + "order": 68, + "type": "content" + }, + { + "text": "to ", + "page": 1, + "order": 69, + "type": "content" + }, + { + "text": "inclusive ", + "page": 1, + "order": 70, + "type": "content" + }, + { + "text": " than their ", + "page": 1, + "order": 71, + "type": "content" + }, + { + "text": "dominant females did actually bias). Instead they could only show ", + "page": 1, + "order": 72, + "type": "content" + }, + { + "text": "that dominant females produce more sons; and that males with ", + "page": 1, + "order": 73, + "type": "content" + }, + { + "text": "more offspring had more dominant mothers. Thus, the most ", + "page": 1, + "order": 74, + "type": "content" + }, + { + "text": "successful males could just as easily have come from the dominant ", + "page": 1, + "order": 75, + "type": "content" + }, + { + "text": "dams who only invest in one \u2018super son\u2019 offspring (which would ", + "page": 1, + "order": 76, + "type": "content" + }, + { + "text": "falsify the hypothesis). As a result, the empirical work in SR ", + "page": 1, + "order": 77, + "type": "content" + }, + { + "text": "manipulation has come under increasing criticism in recent years ", + "page": 1, + "order": 78, + "type": "content" + }, + { + "text": "(e.g. [3,11]), not least because other predicted effects have been ", + "page": 1, + "order": 79, + "type": "content" + }, + { + "text": "much more elusive. In particular, SR theory predicts that males ", + "page": 1, + "order": 80, + "type": "content" + }, + { + "text": "should also control birth SR [2] (and arguably the mechanisms are ", + "page": 1, + "order": 81, + "type": "content" + }, + { + "text": "far more straightforward for them to do so in mammals [12]), but ", + "page": 1, + "order": 82, + "type": "content" + }, + { + "text": "to date examples have been very rare [12,13]. ", + "page": 1, + "order": 83, + "type": "content" + }, + { + "text": "Given the power of SR manipulation\u2019s theoretical argument, ", + "page": 1, + "order": 84, + "type": "content" + }, + { + "text": "the compelling but circumstantial field data in the literature, and ", + "page": 1, + "order": 85, + "type": "content" + }, + { + "text": "the implications for basic reproductive physiology; our goal was to ", + "page": 1, + "order": 86, + "type": "content" + }, + { + "text": "test the central, yet untested, predictions of SR manipulation ", + "page": 1, + "order": 87, + "type": "content" + }, + { + "text": "theory \u2013 that skewing birth SRs enhances parental fitness and that ", + "page": 1, + "order": 88, + "type": "content" + }, + { + "text": "offspring of the favored sex out-reproduce their peers. To do so ", + "page": 1, + "order": 89, + "type": "content" + }, + { + "text": "required overcoming the hurdle of obtaining the three-generation ", + "page": 1, + "order": 90, + "type": "content" + }, + { + "text": "pedigree required. Our solution was to use 90 years of breeding ", + "page": 1, + "order": 91, + "type": "content" + }, + { + "text": "records from San Diego Zoo Global (SDZG) to reconstruct the ", + "page": 1, + "order": 92, + "type": "content" + }, + { + "text": "complete three-generation pedigrees for 198 species of", + "page": 1, + "order": 93, + "type": "content" + }, + { + "text": "Perissodactyla", + "page": 1, + "order": 94, + "type": "content" + }, + { + "text": "who ", + "page": 1, + "order": 95, + "type": "content" + }, + { + "text": "specifically via disproportionate success of the individual favored ", + "page": 1, + "order": 96, + "type": "content" + }, + { + "text": "offspring. To our knowledge this is the first demonstration of the ", + "page": 1, + "order": 97, + "type": "content" + }, + { + "text": "key prediction of SR manipulation theory in mammals, vindicat- ", + "page": 1, + "order": 98, + "type": "content" + }, + { + "text": "ing the earlier classic field studies that could not build the three- ", + "page": 1, + "order": 99, + "type": "content" + }, + { + "text": "generation pedigrees required. ", + "page": 1, + "order": 100, + "type": "content" + }, + { + "text": "Materials and Methods ", + "page": 1, + "order": 101, + "type": "content" + }, + { + "text": "Ethics Statement ", + "page": 1, + "order": 102, + "type": "content" + }, + { + "text": "Prior to data collection, we confirmed with Purdue University\u2019s ", + "page": 1, + "order": 103, + "type": "content" + }, + { + "text": "Institutional Animal Care and Use Committee that no ethical ", + "page": 1, + "order": 104, + "type": "content" + }, + { + "text": "approval was required for this kind of study; data was collected ", + "page": 1, + "order": 105, + "type": "content" + }, + { + "text": "using historical records. ", + "page": 1, + "order": 106, + "type": "content" + }, + { + "text": "Source Records, Subjects, Exclusion criteria, and Data ", + "page": 1, + "order": 107, + "type": "content" + }, + { + "text": "Processing ", + "page": 1, + "order": 108, + "type": "content" + }, + { + "text": "Using breeding records from San Diego Zoo Global (SDZG), ", + "page": 1, + "order": 109, + "type": "content" + }, + { + "text": "we compiled data on 38,075 individuals from 678 mammalian ", + "page": 1, + "order": 110, + "type": "content" + }, + { + "text": "species spanning the", + "page": 1, + "order": 111, + "type": "content" + }, + { + "text": "Primates", + "page": 1, + "order": 112, + "type": "content" + }, + { + "text": "generation) only including those for whom we could follow the ", + "page": 1, + "order": 113, + "type": "content" + }, + { + "text": "breeding of all their children (the F1 generation, totaling 11,909 ", + "page": 1, + "order": 114, + "type": "content" + }, + { + "text": "for granddams; 11,563 for grandsires) to calculate the F0\u2019s success ", + "page": 1, + "order": 115, + "type": "content" + }, + { + "text": "as the number of grandchildren produced (the F2 generation, ", + "page": 1, + "order": 116, + "type": "content" + }, + { + "text": "totaling 16,553 for granddams, 12,895 for grandsires). This ", + "page": 1, + "order": 117, + "type": "content" + }, + { + "text": "measure of success lets us test the most global prediction of SR ", + "page": 1, + "order": 118, + "type": "content" + }, + { + "text": "manipulation theory \u2013 that F0 individuals which have biased birth ", + "page": 1, + "order": 119, + "type": "content" + }, + { + "text": "SR will have more grandchildren. We also calculated F0 success as ", + "page": 1, + "order": 120, + "type": "content" + }, + { + "text": "the grandchildren (F2) born per each of their reproductive F1 ", + "page": 1, + "order": 121, + "type": "content" + }, + { + "text": "offspring; which explicitly examines success via the biased sex, and ", + "page": 1, + "order": 122, + "type": "content" + }, + { + "text": "accounts for those F1 individuals that do not breed, and tests the ", + "page": 1, + "order": 123, + "type": "content" + }, + { + "text": "most explicit prediction of SR manipulation \u2013 that F0s who bias ", + "page": 1, + "order": 124, + "type": "content" + }, + { + "text": "increase F2 success through F1 offspring who outperform their ", + "page": 1, + "order": 125, + "type": "content" + }, + { + "text": "peers. This resulted in pedigrees for 1627 granddams and 703 ", + "page": 1, + "order": 126, + "type": "content" + }, + { + "text": "grandsires. F1 offspring were counted for each grandparent, to ", + "page": 1, + "order": 127, + "type": "content" + }, + { + "text": "calculate their lifetime birth SR. These birth SRs were corrected ", + "page": 1, + "order": 128, + "type": "content" + }, + { + "text": "for the role of chance (a 100% male birth SR is much more ", + "page": 1, + "order": 129, + "type": "content" + }, + { + "text": "impressive given six offspring than three) by expressing them as", + "page": 1, + "order": 130, + "type": "content" + }, + { + "text": "scores, following classic experimental work on birth SR [6]. The ", + "page": 1, + "order": 131, + "type": "content" + }, + { + "text": "Z-", + "page": 1, + "order": 132, + "type": "content" + }, + { + "text": "score, or normal approximation to the binomial, calculated from ", + "page": 1, + "order": 133, + "type": "content" + }, + { + "text": "2 ", + "page": 1, + "order": 134, + "type": "content" + }, + { + "text": " Carnivora", + "page": 1, + "order": 135, + "type": "content" + }, + { + "text": ",", + "page": 1, + "order": 136, + "type": "content" + }, + { + "text": "biased their ", + "page": 1, + "order": 137, + "type": "content" + }, + { + "text": ". We constructed pedigrees for grandparents (the F0 ", + "page": 1, + "order": 138, + "type": "content" + }, + { + "text": "Biased Birth Sex Ratios Lead to More Grandchildren ", + "page": 1, + "order": 139, + "type": "content" + }, + { + "text": " Primates.", + "page": 1, + "order": 140, + "type": "content" + }, + { + "text": ", and", + "page": 1, + "order": 141, + "type": "content" + }, + { + "text": "birth ", + "page": 1, + "order": 142, + "type": "content" + }, + { + "text": "SR gained ", + "page": 1, + "order": 143, + "type": "content" + }, + { + "text": " Artiodactyla", + "page": 1, + "order": 144, + "type": "content" + }, + { + "text": "July 2013 | Volume 8 | Issue 7 | e67867 ", + "page": 1, + "order": 145, + "type": "content" + }, + { + "text": " Grandmothers and Grandsires ", + "page": 1, + "order": 146, + "type": "content" + }, + { + "text": "more grandchildren ", + "page": 1, + "order": 147, + "type": "content" + }, + { + "text": " Perissodactyla", + "page": 1, + "order": 148, + "type": "content" + }, + { + "text": ",", + "page": 1, + "order": 149, + "type": "content" + }, + { + "text": " Artiodactyla", + "page": 1, + "order": 150, + "type": "content" + }, + { + "text": " Carnivora", + "page": 1, + "order": 151, + "type": "content" + }, + { + "text": ",", + "page": 1, + "order": 152, + "type": "content" + }, + { + "text": ", ", + "page": 1, + "order": 153, + "type": "content" + }, + { + "text": "\u2013 ", + "page": 1, + "order": 154, + "type": "content" + }, + { + "text": ", and ", + "page": 1, + "order": 155, + "type": "content" + }, + { + "text": " Z- ", + "page": 1, + "order": 156, + "type": "content" + }, + { + "text": "observed and expected proportions, is given by [14] (and given ", + "page": 2, + "order": 0, + "type": "content" + }, + { + "text": "Fisher\u2019s argument for a population level zygotic SR of 50:50, ", + "page": 2, + "order": 1, + "type": "content" + }, + { + "text": "setting the expected birth SR = 0.5): ", + "page": 2, + "order": 2, + "type": "content" + }, + { + "text": "We calculated the lifetime birth SR, not the per-litter SR to ", + "page": 2, + "order": 3, + "type": "content" + }, + { + "text": "allow for a fair comparison between the monotocous and ", + "page": 2, + "order": 4, + "type": "content" + }, + { + "text": "polytocous species in the data set. A per-litter SR would be ", + "page": 2, + "order": 5, + "type": "content" + }, + { + "text": "dichotomous for monotocous species, but continuous for polyto- ", + "page": 2, + "order": 6, + "type": "content" + }, + { + "text": "cous species. The lifetime SR avoids this confound, but means that ", + "page": 2, + "order": 7, + "type": "content" + }, + { + "text": "we assume that females\u2019 mean lifetime SR is meaningful. This is a ", + "page": 2, + "order": 8, + "type": "content" + }, + { + "text": "conservative assumption: the analysis will pick up females who ", + "page": 2, + "order": 9, + "type": "content" + }, + { + "text": "consistently bias across their lives, but will miss out on the litter- ", + "page": 2, + "order": 10, + "type": "content" + }, + { + "text": "level information from females who might have a one-off ", + "page": 2, + "order": 11, + "type": "content" + }, + { + "text": "opportunity to produce a single litter with highly successful sons ", + "page": 2, + "order": 12, + "type": "content" + }, + { + "text": "(or daughters). Thus, as with all of our analytical choices, we opted ", + "page": 2, + "order": 13, + "type": "content" + }, + { + "text": "for the risk of a false negative, rather than the risk of a false ", + "page": 2, + "order": 14, + "type": "content" + }, + { + "text": "positive. ", + "page": 2, + "order": 15, + "type": "content" + }, + { + "text": "Statistical Methods ", + "page": 2, + "order": 16, + "type": "content" + }, + { + "text": "Blocking by Species nested within Order, F0 animals\u2019", + "page": 2, + "order": 17, + "type": "content" + }, + { + "text": "birth SRs were regressed against the total number of F2 offspring ", + "page": 2, + "order": 18, + "type": "content" + }, + { + "text": "(total grandchildren); and also, the average number of F2 ", + "page": 2, + "order": 19, + "type": "content" + }, + { + "text": "grandoffspring produced by each F1 offspring of the favored sex. ", + "page": 2, + "order": 20, + "type": "content" + }, + { + "text": "Including Species in the analysis identifies F0 individuals as ", + "page": 2, + "order": 21, + "type": "content" + }, + { + "text": "belonging to the same species, which avoids pseudoreplication, ", + "page": 2, + "order": 22, + "type": "content" + }, + { + "text": "and also ensures that the results for", + "page": 2, + "order": 23, + "type": "content" + }, + { + "text": "the mean within-species regression. Analyses were repeated with ", + "page": 2, + "order": 24, + "type": "content" + }, + { + "text": "controls for human management namely: blocking for the year in ", + "page": 2, + "order": 25, + "type": "content" + }, + { + "text": "which each F0 subject first bred and its interaction with Order ", + "page": 2, + "order": 26, + "type": "content" + }, + { + "text": "(since SDZG breeding regimes changed over the decades); and for ", + "page": 2, + "order": 27, + "type": "content" + }, + { + "text": "the proportion of F1 offspring bred (which would reflect the ", + "page": 2, + "order": 28, + "type": "content" + }, + { + "text": "perceived genetic value of a grandparent). All analyses yielded the ", + "page": 2, + "order": 29, + "type": "content" + }, + { + "text": "same ", + "page": 2, + "order": 30, + "type": "content" + }, + { + "text": "conservative analyses including all controls for management. All ", + "page": 2, + "order": 31, + "type": "content" + }, + { + "text": "analyses were initially performed including interactions of", + "page": 2, + "order": 32, + "type": "content" + }, + { + "text": "and Order, to test for different mean relationships in the different ", + "page": 2, + "order": 33, + "type": "content" + }, + { + "text": "taxa. However none of these interactions were significant, and ", + "page": 2, + "order": 34, + "type": "content" + }, + { + "text": "were therefore removed from the final analysis to ensure ", + "page": 2, + "order": 35, + "type": "content" + }, + { + "text": "marginality [15]. For granddams, 44 of 193 species were ", + "page": 2, + "order": 36, + "type": "content" + }, + { + "text": "represented by a single female; and for grandsires, 67 of 197 ", + "page": 2, + "order": 37, + "type": "content" + }, + { + "text": "species were represented by a single male. These data points were ", + "page": 2, + "order": 38, + "type": "content" + }, + { + "text": "inherently excluded by the analysis, as it tested for within-species ", + "page": 2, + "order": 39, + "type": "content" + }, + { + "text": "effects (final distributions are provided in Materials S1). All ", + "page": 2, + "order": 40, + "type": "content" + }, + { + "text": "analyses were performed as GLMs in JMP 9.0 for Windows. The ", + "page": 2, + "order": 41, + "type": "content" + }, + { + "text": "assumptions of GLM (normality of error, homogeneity of variance, ", + "page": 2, + "order": 42, + "type": "content" + }, + { + "text": "and linearity) were confirmed", + "page": 2, + "order": 43, + "type": "content" + }, + { + "text": "applied as needed [15]. ", + "page": 2, + "order": 44, + "type": "content" + }, + { + "text": "Results ", + "page": 2, + "order": 45, + "type": "content" + }, + { + "text": "F1 population-level birth SRs proved slightly female biased (for ", + "page": 2, + "order": 46, + "type": "content" + }, + { + "text": "granddams 47.5% of F1 offspring were male). Birth SR varied ", + "page": 2, + "order": 47, + "type": "content" + }, + { + "text": "greatly across F0 subjects (86.8% of variance in SR occurred ", + "page": 2, + "order": 48, + "type": "content" + }, + { + "text": "within-species for granddams, and 72.4%for grandsires; see ", + "page": 2, + "order": 49, + "type": "content" + }, + { + "text": "Table 1 for particularly variable species) and this variation did ", + "page": 2, + "order": 50, + "type": "content" + }, + { + "text": "indeed have adaptive consequences in general across the range of ", + "page": 2, + "order": 51, + "type": "content" + }, + { + "text": "species in the data set. Granddams who biased their birth SR ", + "page": 2, + "order": 52, + "type": "content" + }, + { + "text": "towards ", + "page": 2, + "order": 53, + "type": "content" + }, + { + "text": "F", + "page": 2, + "order": 54, + "type": "content" + }, + { + "text": "1,1427", + "page": 2, + "order": 55, + "type": "content" + }, + { + "text": "PLOS ONE | www.plosone.org ", + "page": 2, + "order": 56, + "type": "content" + }, + { + "text": "pattern ", + "page": 2, + "order": 57, + "type": "content" + }, + { + "text": "of ", + "page": 2, + "order": 58, + "type": "content" + }, + { + "text": "sons ", + "page": 2, + "order": 59, + "type": "content" + }, + { + "text": "gained ", + "page": 2, + "order": 60, + "type": "content" + }, + { + "text": ",", + "page": 2, + "order": 61, + "type": "content" + }, + { + "text": " P", + "page": 2, + "order": 62, + "type": "content" + }, + { + "text": " = 26.45:", + "page": 2, + "order": 63, + "type": "content" + }, + { + "text": "Observed", + "page": 2, + "order": 64, + "type": "content" + }, + { + "text": "q ", + "page": 2, + "order": 65, + "type": "content" + }, + { + "text": "\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03\ufb03 ", + "page": 2, + "order": 66, + "type": "content" + }, + { + "text": "~", + "page": 2, + "order": 67, + "type": "content" + }, + { + "text": "Z", + "page": 2, + "order": 68, + "type": "content" + }, + { + "text": " ", + "page": 2, + "order": 69, + "type": "content" + }, + { + "text": "2", + "page": 2, + "order": 70, + "type": "content" + }, + { + "text": "Expected", + "page": 2, + "order": 71, + "type": "content" + }, + { + "text": "results. ", + "page": 2, + "order": 72, + "type": "content" + }, + { + "text": "Therefore, ", + "page": 2, + "order": 73, + "type": "content" + }, + { + "text": " post hoc", + "page": 2, + "order": 74, + "type": "content" + }, + { + "text": "more ", + "page": 2, + "order": 75, + "type": "content" + }, + { + "text": "grandoffspring ", + "page": 2, + "order": 76, + "type": "content" + }, + { + "text": " N", + "page": 2, + "order": 77, + "type": "content" + }, + { + "text": "0.0001;", + "page": 2, + "order": 78, + "type": "content" + }, + { + "text": " = 1627 granddams;", + "page": 2, + "order": 79, + "type": "content" + }, + { + "text": "{", + "page": 2, + "order": 80, + "type": "content" + }, + { + "text": "Expected ", + "page": 2, + "order": 81, + "type": "content" + }, + { + "text": "\u00f0 ", + "page": 2, + "order": 82, + "type": "content" + }, + { + "text": "\u00de ", + "page": 2, + "order": 83, + "type": "content" + }, + { + "text": "{", + "page": 2, + "order": 84, + "type": "content" + }, + { + "text": " 1", + "page": 2, + "order": 85, + "type": "content" + }, + { + "text": "Expected ", + "page": 2, + "order": 86, + "type": "content" + }, + { + "text": "N ", + "page": 2, + "order": 87, + "type": "content" + }, + { + "text": " Z", + "page": 2, + "order": 88, + "type": "content" + }, + { + "text": "-scored birth SR represent ", + "page": 2, + "order": 89, + "type": "content" + }, + { + "text": "we ", + "page": 2, + "order": 90, + "type": "content" + }, + { + "text": " and suitable transformations ", + "page": 2, + "order": 91, + "type": "content" + }, + { + "text": " Z-", + "page": 2, + "order": 92, + "type": "content" + }, + { + "text": "scored ", + "page": 2, + "order": 93, + "type": "content" + }, + { + "text": "present ", + "page": 2, + "order": 94, + "type": "content" + }, + { + "text": "the ", + "page": 2, + "order": 95, + "type": "content" + }, + { + "text": " Z", + "page": 2, + "order": 96, + "type": "content" + }, + { + "text": "in ", + "page": 2, + "order": 97, + "type": "content" + }, + { + "text": "total ", + "page": 2, + "order": 98, + "type": "content" + }, + { + "text": "(GLM: ", + "page": 2, + "order": 99, + "type": "content" + }, + { + "text": " Figure 1A", + "page": 2, + "order": 100, + "type": "content" + }, + { + "text": "did ", + "page": 2, + "order": 101, + "type": "content" + }, + { + "text": "F", + "page": 2, + "order": 102, + "type": "content" + }, + { + "text": "1,499", + "page": 2, + "order": 103, + "type": "content" + }, + { + "text": "most strongly male-biased granddams and grandsires produced ", + "page": 2, + "order": 104, + "type": "content" + }, + { + "text": "respectively 29% and 25% more grandoffspring than non-skewing ", + "page": 2, + "order": 105, + "type": "content" + }, + { + "text": "conspecifics. The more male-biased a granddam\u2019s birth SR, the ", + "page": 2, + "order": 106, + "type": "content" + }, + { + "text": "more ", + "page": 2, + "order": 107, + "type": "content" + }, + { + "text": "F", + "page": 2, + "order": 108, + "type": "content" + }, + { + "text": "1,1260", + "page": 2, + "order": 109, + "type": "content" + }, + { + "text": "the sons of the most male-biasing granddams were 2.7 times as ", + "page": 2, + "order": 110, + "type": "content" + }, + { + "text": "fecund as those of granddams with a 50:50 bias. Similar effects ", + "page": 2, + "order": 111, + "type": "content" + }, + { + "text": "held for grandsires (GLM:", + "page": 2, + "order": 112, + "type": "content" + }, + { + "text": "grandsires;", + "page": 2, + "order": 113, + "type": "content" + }, + { + "text": "birth SR, the more grandoffspring she gained from each daughter ", + "page": 2, + "order": 114, + "type": "content" + }, + { + "text": "(GLM: ", + "page": 2, + "order": 115, + "type": "content" + }, + { + "text": "Figure 1E", + "page": 2, + "order": 116, + "type": "content" + }, + { + "text": "strongest F0 female-biasing females were 1.2 times as fecund as ", + "page": 2, + "order": 117, + "type": "content" + }, + { + "text": "those of non-biasing females. The SR bias of grandsires had no ", + "page": 2, + "order": 118, + "type": "content" + }, + { + "text": "effect on the number of grandchildren gained from each daughter. ", + "page": 2, + "order": 119, + "type": "content" + }, + { + "text": "(GLM: ", + "page": 2, + "order": 120, + "type": "content" + }, + { + "text": "Figure 1F", + "page": 2, + "order": 121, + "type": "content" + }, + { + "text": "Discussion ", + "page": 2, + "order": 122, + "type": "content" + }, + { + "text": "These data clearly demonstrate the ultimate reason why parents ", + "page": 2, + "order": 123, + "type": "content" + }, + { + "text": "control birth SR: parents who are able to judge the future success ", + "page": 2, + "order": 124, + "type": "content" + }, + { + "text": "of their first generation offspring and bias their birth SR ", + "page": 2, + "order": 125, + "type": "content" + }, + { + "text": "accordingly have a clear F2 fitness advantage over those who ", + "page": 2, + "order": 126, + "type": "content" + }, + { + "text": "cannot. Therefore, as first clearly postulated over 40 years ago [2], ", + "page": 2, + "order": 127, + "type": "content" + }, + { + "text": "but to our knowledge demonstrated here for the first time, sex ", + "page": 2, + "order": 128, + "type": "content" + }, + { + "text": "ratio manipulation is a widespread and highly adaptive evolution- ", + "page": 2, + "order": 129, + "type": "content" + }, + { + "text": "ary strategy in mammals. The most global prediction of SR ", + "page": 2, + "order": 130, + "type": "content" + }, + { + "text": "manipulation theory \u2013 that individuals who manipulate their birth ", + "page": 2, + "order": 131, + "type": "content" + }, + { + "text": "SR will have more grandchildren through the improved repro- ", + "page": 2, + "order": 132, + "type": "content" + }, + { + "text": "ductive output of F1 offspring of the biased sex \u2013 was thus ", + "page": 2, + "order": 133, + "type": "content" + }, + { + "text": "supported. Specifically, the sons of granddams with male-biased ", + "page": 2, + "order": 134, + "type": "content" + }, + { + "text": "birth SRs out-perform their peers, yielding these granddams more ", + "page": 2, + "order": 135, + "type": "content" + }, + { + "text": "grandchildren. The same holds for grandsires. Furthermore these ", + "page": 2, + "order": 136, + "type": "content" + }, + { + "text": "data, to our knowledge, show for the first time that the daughters ", + "page": 2, + "order": 137, + "type": "content" + }, + { + "text": "of female-biasing granddams likewise outperform their peers. The ", + "page": 2, + "order": 138, + "type": "content" + }, + { + "text": "most ", + "page": 2, + "order": 139, + "type": "content" + }, + { + "text": "differential effects seen in the analyses of success via the F1 sex are ", + "page": 2, + "order": 140, + "type": "content" + }, + { + "text": "consistent with existing understanding of factors influencing birth ", + "page": 2, + "order": 141, + "type": "content" + }, + { + "text": "-score ", + "page": 2, + "order": 142, + "type": "content" + }, + { + "text": "SR in granddams [5\u20137,13,16\u201322]. Thus, the lack of influence of ", + "page": 2, + "order": 143, + "type": "content" + }, + { + "text": "grandsire BSR on F2 success via F1 daughters was expected, and ", + "page": 2, + "order": 144, + "type": "content" + }, + { + "text": "the very weak effect of granddam BSR on F2 success via F1 ", + "page": 2, + "order": 145, + "type": "content" + }, + { + "text": "daughters likely reflects a subset of \u2018special-case\u2019 species, rather ", + "page": 2, + "order": 146, + "type": "content" + }, + { + "text": "than a general effect. ", + "page": 2, + "order": 147, + "type": "content" + }, + { + "text": "The use of captive populations warrants comment, as it is a ", + "page": 2, + "order": 148, + "type": "content" + }, + { + "text": "double-edged sword. Because the populations are captive, and ", + "page": 2, + "order": 149, + "type": "content" + }, + { + "text": "because the provenance of individual animals is so critical in ", + "page": 2, + "order": 150, + "type": "content" + }, + { + "text": "captive breeding, we can reconstruct pedigrees across a breadth of ", + "page": 2, + "order": 151, + "type": "content" + }, + { + "text": "species and to a depth of generations that would be impossible in ", + "page": 2, + "order": 152, + "type": "content" + }, + { + "text": "the wild. Indeed, the previous lack of a strong test of SR ", + "page": 2, + "order": 153, + "type": "content" + }, + { + "text": "manipulation in terms of grandchildren is itself compelling ", + "page": 2, + "order": 154, + "type": "content" + }, + { + "text": "evidence for just how difficult it is to produce a complete three- ", + "page": 2, + "order": 155, + "type": "content" + }, + { + "text": "generation pedigree in a wild mammalian population. Such a data ", + "page": 2, + "order": 156, + "type": "content" + }, + { + "text": "set is obviously not impossible, but it is sufficiently impractical to ", + "page": 2, + "order": 157, + "type": "content" + }, + { + "text": "have eluded researchers for forty years. Thus using data from ", + "page": 2, + "order": 158, + "type": "content" + }, + { + "text": "captive animals is not so much of an advantage, but currently a ", + "page": 2, + "order": 159, + "type": "content" + }, + { + "text": "necessity. Zoo populations represent the best choice for a sample ", + "page": 2, + "order": 160, + "type": "content" + }, + { + "text": "population compared to farm or laboratory animals, because they ", + "page": 2, + "order": 161, + "type": "content" + }, + { + "text": "provide a breadth of species, and they enjoy a more naturalistic ", + "page": 2, + "order": 162, + "type": "content" + }, + { + "text": "environment. This last point however, reveals the downside of ", + "page": 2, + "order": 163, + "type": "content" + }, + { + "text": "working with zoo populations \u2013 that they are still managed ", + "page": 2, + "order": 164, + "type": "content" + }, + { + "text": "populations where breeding is to a degree under human control, ", + "page": 2, + "order": 165, + "type": "content" + }, + { + "text": "), as ", + "page": 2, + "order": 166, + "type": "content" + }, + { + "text": "and where the environment may differ from captivity in ways that ", + "page": 2, + "order": 167, + "type": "content" + }, + { + "text": "3 ", + "page": 2, + "order": 168, + "type": "content" + }, + { + "text": "grandsires ", + "page": 2, + "order": 169, + "type": "content" + }, + { + "text": " P", + "page": 2, + "order": 170, + "type": "content" + }, + { + "text": " = 6.553:", + "page": 2, + "order": 171, + "type": "content" + }, + { + "text": "grandoffspring ", + "page": 2, + "order": 172, + "type": "content" + }, + { + "text": " P", + "page": 2, + "order": 173, + "type": "content" + }, + { + "text": " = 194.9:", + "page": 2, + "order": 174, + "type": "content" + }, + { + "text": " Figure 1D", + "page": 2, + "order": 175, + "type": "content" + }, + { + "text": "F", + "page": 2, + "order": 176, + "type": "content" + }, + { + "text": " = 4.891: ", + "page": 2, + "order": 177, + "type": "content" + }, + { + "text": "1,1390", + "page": 2, + "order": 178, + "type": "content" + }, + { + "text": "); effects were smaller however \u2013 daughters of the ", + "page": 2, + "order": 179, + "type": "content" + }, + { + "text": "F", + "page": 2, + "order": 180, + "type": "content" + }, + { + "text": " = 0.0052: ", + "page": 2, + "order": 181, + "type": "content" + }, + { + "text": "1,476", + "page": 2, + "order": 182, + "type": "content" + }, + { + "text": "). ", + "page": 2, + "order": 183, + "type": "content" + }, + { + "text": "Biased Birth Sex Ratios Lead to More Grandchildren ", + "page": 2, + "order": 184, + "type": "content" + }, + { + "text": "who ", + "page": 2, + "order": 185, + "type": "content" + }, + { + "text": "male-biased ", + "page": 2, + "order": 186, + "type": "content" + }, + { + "text": ",", + "page": 2, + "order": 187, + "type": "content" + }, + { + "text": " N", + "page": 2, + "order": 188, + "type": "content" + }, + { + "text": "0.0108;", + "page": 2, + "order": 189, + "type": "content" + }, + { + "text": " = 703 grandsires;", + "page": 2, + "order": 190, + "type": "content" + }, + { + "text": "she ", + "page": 2, + "order": 191, + "type": "content" + }, + { + "text": "gained ", + "page": 2, + "order": 192, + "type": "content" + }, + { + "text": ",", + "page": 2, + "order": 193, + "type": "content" + }, + { + "text": " N", + "page": 2, + "order": 194, + "type": "content" + }, + { + "text": "0.0001;", + "page": 2, + "order": 195, + "type": "content" + }, + { + "text": " F", + "page": 2, + "order": 196, + "type": "content" + }, + { + "text": "). The more female-biased a granddam\u2019s ", + "page": 2, + "order": 197, + "type": "content" + }, + { + "text": "P", + "page": 2, + "order": 198, + "type": "content" + }, + { + "text": " = 0.0272; ", + "page": 2, + "order": 199, + "type": "content" + }, + { + "text": "P", + "page": 2, + "order": 200, + "type": "content" + }, + { + "text": "July 2013 | Volume 8 | Issue 7 | e67867 ", + "page": 2, + "order": 201, + "type": "content" + }, + { + "text": "their ", + "page": 2, + "order": 202, + "type": "content" + }, + { + "text": "from ", + "page": 2, + "order": 203, + "type": "content" + }, + { + "text": " = 1454 granddams;", + "page": 2, + "order": 204, + "type": "content" + }, + { + "text": " = 27.53:", + "page": 2, + "order": 205, + "type": "content" + }, + { + "text": "1,468", + "page": 2, + "order": 206, + "type": "content" + }, + { + "text": "N", + "page": 2, + "order": 207, + "type": "content" + }, + { + "text": " = 1558 ", + "page": 2, + "order": 208, + "type": "content" + }, + { + "text": "N", + "page": 2, + "order": 209, + "type": "content" + }, + { + "text": " = 0.9426; ", + "page": 2, + "order": 210, + "type": "content" + }, + { + "text": "birth ", + "page": 2, + "order": 211, + "type": "content" + }, + { + "text": "SR ", + "page": 2, + "order": 212, + "type": "content" + }, + { + "text": " Figure 1B", + "page": 2, + "order": 213, + "type": "content" + }, + { + "text": "each ", + "page": 2, + "order": 214, + "type": "content" + }, + { + "text": "son ", + "page": 2, + "order": 215, + "type": "content" + }, + { + "text": " Figure 1C", + "page": 2, + "order": 216, + "type": "content" + }, + { + "text": ",", + "page": 2, + "order": 217, + "type": "content" + }, + { + "text": " P", + "page": 2, + "order": 218, + "type": "content" + }, + { + "text": " N", + "page": 2, + "order": 219, + "type": "content" + }, + { + "text": "0.0001;", + "page": 2, + "order": 220, + "type": "content" + }, + { + "text": "granddams; ", + "page": 2, + "order": 221, + "type": "content" + }, + { + "text": " = 678 ", + "page": 2, + "order": 222, + "type": "content" + }, + { + "text": "grandsires; ", + "page": 2, + "order": 223, + "type": "content" + }, + { + "text": "(GLM: ", + "page": 2, + "order": 224, + "type": "content" + }, + { + "text": "). The ", + "page": 2, + "order": 225, + "type": "content" + }, + { + "text": "(GLM: ", + "page": 2, + "order": 226, + "type": "content" + }, + { + "text": "): ", + "page": 2, + "order": 227, + "type": "content" + }, + { + "text": " = 678 ", + "page": 2, + "order": 228, + "type": "content" + }, + { + "text": "Figure 1. Grandparents who bias the sex of the offspring, have more successful offspring, gaining more grandchildren. A", + "page": 3, + "order": 0, + "type": "content" + }, + { + "text": "Granddams and", + "page": 3, + "order": 1, + "type": "content" + }, + { + "text": "P =", + "page": 3, + "order": 2, + "type": "content" + }, + { + "text": " 0.0108, respectively). Birth SR is shown as a", + "page": 3, + "order": 3, + "type": "content" + }, + { + "text": "Z-", + "page": 3, + "order": 4, + "type": "content" + }, + { + "text": "score).", + "page": 3, + "order": 5, + "type": "content" + }, + { + "text": "Granddams who biased birth SR towards females had greater success specifically via F1 females (", + "page": 3, + "order": 6, + "type": "content" + }, + { + "text": "biasing grandsires (", + "page": 3, + "order": 7, + "type": "content" + }, + { + "text": "10th percentiles by", + "page": 3, + "order": 8, + "type": "content" + }, + { + "text": "squares regression line partialled for the controlling variables. In", + "page": 3, + "order": 9, + "type": "content" + }, + { + "text": "and grandsire success is shown as the grandchildren (F2) born per each of their F1offspring born of a given sex (i.e. the mean reproductive output of ", + "page": 3, + "order": 10, + "type": "content" + }, + { + "text": "the F1 children of each sex). ", + "page": 3, + "order": 11, + "type": "content" + }, + { + "text": "doi:10.1371/journal.pone.0067867.g001 ", + "page": 3, + "order": 12, + "type": "content" + }, + { + "text": "PLOS ONE | www.plosone.org ", + "page": 3, + "order": 13, + "type": "content" + }, + { + "text": " B", + "page": 3, + "order": 14, + "type": "content" + }, + { + "text": ") grandsires who biased birth SR towards males had greater total success measured as total grandchildren produced (", + "page": 3, + "order": 15, + "type": "content" + }, + { + "text": " C", + "page": 3, + "order": 16, + "type": "content" + }, + { + "text": ") Granddams, and", + "page": 3, + "order": 17, + "type": "content" + }, + { + "text": "P", + "page": 3, + "order": 18, + "type": "content" + }, + { + "text": " Z-", + "page": 3, + "order": 19, + "type": "content" + }, + { + "text": " D", + "page": 3, + "order": 20, + "type": "content" + }, + { + "text": ") grandsires, who biased birth SR towards males had greater success specifically via F1 males (for both,", + "page": 3, + "order": 21, + "type": "content" + }, + { + "text": " = 0.9426), (nor did they have more total grandchildren overall; see text). For clearer data visualization, the data were split into ", + "page": 3, + "order": 22, + "type": "content" + }, + { + "text": "score, and plotted values are least-squares means and standard errors within those percentiles. The solid line indicates the least- ", + "page": 3, + "order": 23, + "type": "content" + }, + { + "text": " Z-", + "page": 3, + "order": 24, + "type": "content" + }, + { + "text": "score, to control for number of F1 offspring (the X-axes also give examples of male biases for a given ", + "page": 3, + "order": 25, + "type": "content" + }, + { + "text": " A", + "page": 3, + "order": 26, + "type": "content" + }, + { + "text": " and", + "page": 3, + "order": 27, + "type": "content" + }, + { + "text": " B", + "page": 3, + "order": 28, + "type": "content" + }, + { + "text": ", the Y-axes shows F0 success as total grandchildren born. In", + "page": 3, + "order": 29, + "type": "content" + }, + { + "text": "4 ", + "page": 3, + "order": 30, + "type": "content" + }, + { + "text": "Biased Birth Sex Ratios Lead to More Grandchildren ", + "page": 3, + "order": 31, + "type": "content" + }, + { + "text": "P =", + "page": 3, + "order": 32, + "type": "content" + }, + { + "text": " 0.0272), but no effects were found for female- ", + "page": 3, + "order": 33, + "type": "content" + }, + { + "text": "July 2013 | Volume 8 | Issue 7 | e67867 ", + "page": 3, + "order": 34, + "type": "content" + }, + { + "text": ",", + "page": 3, + "order": 35, + "type": "content" + }, + { + "text": "P", + "page": 3, + "order": 36, + "type": "content" + }, + { + "text": ",", + "page": 3, + "order": 37, + "type": "content" + }, + { + "text": " P", + "page": 3, + "order": 38, + "type": "content" + }, + { + "text": "0.0001).", + "page": 3, + "order": 39, + "type": "content" + }, + { + "text": " C", + "page": 3, + "order": 40, + "type": "content" + }, + { + "text": "\u2013", + "page": 3, + "order": 41, + "type": "content" + }, + { + "text": "F", + "page": 3, + "order": 42, + "type": "content" + }, + { + "text": ", granddam ", + "page": 3, + "order": 43, + "type": "content" + }, + { + "text": ") ", + "page": 3, + "order": 44, + "type": "content" + }, + { + "text": "0.0001; ", + "page": 3, + "order": 45, + "type": "content" + }, + { + "text": " E", + "page": 3, + "order": 46, + "type": "content" + }, + { + "text": ") ", + "page": 3, + "order": 47, + "type": "content" + }, + { + "text": "Table 1.", + "page": 4, + "order": 0, + "type": "content" + }, + { + "text": "Common name ", + "page": 4, + "order": 1, + "type": "content" + }, + { + "text": "Granddams ", + "page": 4, + "order": 2, + "type": "content" + }, + { + "text": "Vaal Rhebok ", + "page": 4, + "order": 3, + "type": "content" + }, + { + "text": "Sumatran Tiger ", + "page": 4, + "order": 4, + "type": "content" + }, + { + "text": "Red River Hog ", + "page": 4, + "order": 5, + "type": "content" + }, + { + "text": "Sudan Red-fronted Gazelle ", + "page": 4, + "order": 6, + "type": "content" + }, + { + "text": "Gambian Maxwell\u2019s Duiker ", + "page": 4, + "order": 7, + "type": "content" + }, + { + "text": "Grandsires ", + "page": 4, + "order": 8, + "type": "content" + }, + { + "text": "Kenya Impala ", + "page": 4, + "order": 9, + "type": "content" + }, + { + "text": "Indochinese Sika ", + "page": 4, + "order": 10, + "type": "content" + }, + { + "text": "Francois\u2019 Langur ", + "page": 4, + "order": 11, + "type": "content" + }, + { + "text": "East African Black Rhinoceros ", + "page": 4, + "order": 12, + "type": "content" + }, + { + "text": "Nubian Ibex ", + "page": 4, + "order": 13, + "type": "content" + }, + { + "text": "The variance in birth SR was figured for each species. The five species with the greatest variance (i.e. standard deviation", + "page": 4, + "order": 14, + "type": "content" + }, + { + "text": "are listed. Because birth SR is expressed as", + "page": 4, + "order": 15, + "type": "content" + }, + { + "text": "variance in", + "page": 4, + "order": 16, + "type": "content" + }, + { + "text": "doi:10.1371/journal.pone.0067867.t001 ", + "page": 4, + "order": 17, + "type": "content" + }, + { + "text": "present misleading cues to animals in terms of SR manipulation. ", + "page": 4, + "order": 18, + "type": "content" + }, + { + "text": "The level of management, and the qualitative match of the captive ", + "page": 4, + "order": 19, + "type": "content" + }, + { + "text": "to the wild environment, both differ in particular by taxon and ", + "page": 4, + "order": 20, + "type": "content" + }, + { + "text": "between modern", + "page": 4, + "order": 21, + "type": "content" + }, + { + "text": "hoofstock species at SDZG live in a relatively free ranging herd ", + "page": 4, + "order": 22, + "type": "content" + }, + { + "text": "and males may experience direct competition resulting in female ", + "page": 4, + "order": 23, + "type": "content" + }, + { + "text": "mate choice; while primate species may not be provided rival ", + "page": 4, + "order": 24, + "type": "content" + }, + { + "text": "mates simultaneously. However, even in the absence of perceived ", + "page": 4, + "order": 25, + "type": "content" + }, + { + "text": "mate choice, females can often control whether or not they mate, ", + "page": 4, + "order": 26, + "type": "content" + }, + { + "text": "the chance of conception, and", + "page": 4, + "order": 27, + "type": "content" + }, + { + "text": "offspring from different males. Most importantly, however, captive ", + "page": 4, + "order": 28, + "type": "content" + }, + { + "text": "breeding programs track the provenance of potential mates and ", + "page": 4, + "order": 29, + "type": "content" + }, + { + "text": "explicitly attempt to minimize the rate of loss of genetic diversity ", + "page": 4, + "order": 30, + "type": "content" + }, + { + "text": "caused by population bottlenecks (e.g. by limiting the number of ", + "page": 4, + "order": 31, + "type": "content" + }, + { + "text": "mating opportunities given to particular sires). However, for our ", + "page": 4, + "order": 32, + "type": "content" + }, + { + "text": "analyses, such effects should\u2013if anything\u2013produce false negatives; ", + "page": 4, + "order": 33, + "type": "content" + }, + { + "text": "and they certainly could not produce false positives. Thus a ", + "page": 4, + "order": 34, + "type": "content" + }, + { + "text": "misleading environmental cue might cause females to bias their ", + "page": 4, + "order": 35, + "type": "content" + }, + { + "text": "SR, but the resulting biased offspring would not benefit. Similarly, ", + "page": 4, + "order": 36, + "type": "content" + }, + { + "text": "if humans are controlling breeding to maximize genetic diversity ", + "page": 4, + "order": 37, + "type": "content" + }, + { + "text": "then they will curtail the success of high quality males, and boost ", + "page": 4, + "order": 38, + "type": "content" + }, + { + "text": "the success of low quality males. Our results have thus emerged ", + "page": 4, + "order": 39, + "type": "content" + }, + { + "text": "despite a strong potential for adaptive SR effects to be masked in ", + "page": 4, + "order": 40, + "type": "content" + }, + { + "text": "captivity. They are thus extremely conservative, and suggest that ", + "page": 4, + "order": 41, + "type": "content" + }, + { + "text": "were it possible to follow three generations or more in the wild, ", + "page": 4, + "order": 42, + "type": "content" + }, + { + "text": "even stronger effects would be evident. Consequently, the analyses ", + "page": 4, + "order": 43, + "type": "content" + }, + { + "text": "are explicitly designed to capitalize on the strengths of these data, ", + "page": 4, + "order": 44, + "type": "content" + }, + { + "text": "while protecting against the potential weaknesses. Thus, by testing ", + "page": 4, + "order": 45, + "type": "content" + }, + { + "text": "for general birth SR trends across the controlling variables, the ", + "page": 4, + "order": 46, + "type": "content" + }, + { + "text": "analysis exploits the heterogeneity of the data (in terms of species, ", + "page": 4, + "order": 47, + "type": "content" + }, + { + "text": "year of breeding, husbandry systems,", + "page": 4, + "order": 48, + "type": "content" + }, + { + "text": "is general, rather than a specific artifact driven by a particular ", + "page": 4, + "order": 49, + "type": "content" + }, + { + "text": "species or husbandry system. Similarly, by testing for specific ", + "page": 4, + "order": 50, + "type": "content" + }, + { + "text": "predictions via the F1 genders separately, the analyses guard ", + "page": 4, + "order": 51, + "type": "content" + }, + { + "text": "against a general false positive tainting the whole data set. Finally, ", + "page": 4, + "order": 52, + "type": "content" + }, + { + "text": "by testing for specific benefits in F2 success to the F0 grandparents, ", + "page": 4, + "order": 53, + "type": "content" + }, + { + "text": "deriving from an improved success of the biased F1 offspring, we ", + "page": 4, + "order": 54, + "type": "content" + }, + { + "text": "test the common prediction of all SR manipulation theories, and ", + "page": 4, + "order": 55, + "type": "content" + }, + { + "text": "are therefore agnostic as to which of the cues or mechanisms (e.g. ", + "page": 4, + "order": 56, + "type": "content" + }, + { + "text": "PLOS ONE | www.plosone.org ", + "page": 4, + "order": 57, + "type": "content" + }, + { + "text": " Species with notably skewed Birth Sex Ratios. ", + "page": 4, + "order": 58, + "type": "content" + }, + { + "text": " Z-", + "page": 4, + "order": 59, + "type": "content" + }, + { + "text": "score. ", + "page": 4, + "order": 60, + "type": "content" + }, + { + "text": " versus", + "page": 4, + "order": 61, + "type": "content" + }, + { + "text": " historical populations. For instance, many ", + "page": 4, + "order": 62, + "type": "content" + }, + { + "text": " in utero", + "page": 4, + "order": 63, + "type": "content" + }, + { + "text": "Scientific name ", + "page": 4, + "order": 64, + "type": "content" + }, + { + "text": "Pelea capreolus ", + "page": 4, + "order": 65, + "type": "content" + }, + { + "text": "Panthera tigris ", + "page": 4, + "order": 66, + "type": "content" + }, + { + "text": "Potamochoerus porcus ", + "page": 4, + "order": 67, + "type": "content" + }, + { + "text": "Gazella rufifrons ", + "page": 4, + "order": 68, + "type": "content" + }, + { + "text": "Cephalophus maxwellii ", + "page": 4, + "order": 69, + "type": "content" + }, + { + "text": "Aepyceros melampus ", + "page": 4, + "order": 70, + "type": "content" + }, + { + "text": "Cervus Nippon ", + "page": 4, + "order": 71, + "type": "content" + }, + { + "text": "Trachypithecus francoisi ", + "page": 4, + "order": 72, + "type": "content" + }, + { + "text": "Diceros bicornis ", + "page": 4, + "order": 73, + "type": "content" + }, + { + "text": "Capra nubiana ", + "page": 4, + "order": 74, + "type": "content" + }, + { + "text": " Z-", + "page": 4, + "order": 75, + "type": "content" + }, + { + "text": "score, the expected variance for any species = 1. The observed variances are tested against the mean within-species ", + "page": 4, + "order": 76, + "type": "content" + }, + { + "text": " and post natal investment in ", + "page": 4, + "order": 77, + "type": "content" + }, + { + "text": " etc.", + "page": 4, + "order": 78, + "type": "content" + }, + { + "text": ") to ensure that any result ", + "page": 4, + "order": 79, + "type": "content" + }, + { + "text": "Trivers-Willard, or Local Resource Enhancement), might be ", + "page": 4, + "order": 80, + "type": "content" + }, + { + "text": "responsible. ", + "page": 4, + "order": 81, + "type": "content" + }, + { + "text": "Overall, despite a dataset where such effects could be masked by ", + "page": 4, + "order": 82, + "type": "content" + }, + { + "text": "human attempts to control breeding, skewing birth SR is ", + "page": 4, + "order": 83, + "type": "content" + }, + { + "text": "confirmed (thanks to unprecedented sample sizes and complete, ", + "page": 4, + "order": 84, + "type": "content" + }, + { + "text": "accurate counts of grandoffspring) as a widely utilized strategy ", + "page": 4, + "order": 85, + "type": "content" + }, + { + "text": "across captive", + "page": 4, + "order": 86, + "type": "content" + }, + { + "text": "but is likely extended to wild", + "page": 4, + "order": 87, + "type": "content" + }, + { + "text": "newly identify ideal species (those with high variances in birth SR: ", + "page": 4, + "order": 88, + "type": "content" + }, + { + "text": "see Table 1) for future research on proximate mechanisms ", + "page": 4, + "order": 89, + "type": "content" + }, + { + "text": "underlying mammalian SR manipulation, the physiology of which ", + "page": 4, + "order": 90, + "type": "content" + }, + { + "text": "remains unknown [3,10,11]. These findings have additional ", + "page": 4, + "order": 91, + "type": "content" + }, + { + "text": "practical implications too: in captive populations under human ", + "page": 4, + "order": 92, + "type": "content" + }, + { + "text": "control, these individually adaptive strategies may be significantly ", + "page": 4, + "order": 93, + "type": "content" + }, + { + "text": "impacting the long term genetic viability of the species and ", + "page": 4, + "order": 94, + "type": "content" + }, + { + "text": "compromising the captive population as a whole. The increased ", + "page": 4, + "order": 95, + "type": "content" + }, + { + "text": "variability in F2 success between grandsires", + "page": 4, + "order": 96, + "type": "content" + }, + { + "text": "apparent in Figures 1A \u20131D, neatly illustrates the species-level cost ", + "page": 4, + "order": 97, + "type": "content" + }, + { + "text": "of SRM in small populations. Winners of the genetic lottery do so ", + "page": 4, + "order": 98, + "type": "content" + }, + { + "text": "at others\u2019 expense, and a highly successful F1 male over- ", + "page": 4, + "order": 99, + "type": "content" + }, + { + "text": "contributes to the next generation at the species-level cost of the ", + "page": 4, + "order": 100, + "type": "content" + }, + { + "text": "loss of genetic variation from the males that fail to breed. Thus the ", + "page": 4, + "order": 101, + "type": "content" + }, + { + "text": "general tendency of captive species to bias their birth SR ", + "page": 4, + "order": 102, + "type": "content" + }, + { + "text": "demonstrated here (especially in F1 males), combined with the ", + "page": 4, + "order": 103, + "type": "content" + }, + { + "text": "fact that many captive species have male biased BSR [23,24], has ", + "page": 4, + "order": 104, + "type": "content" + }, + { + "text": "the potential to accelerate the loss of genetic diversity from ", + "page": 4, + "order": 105, + "type": "content" + }, + { + "text": "endangered captive-bred species. Accordingly understanding the ", + "page": 4, + "order": 106, + "type": "content" + }, + { + "text": "factors leading to biased birth SR in captive populations, and thus ", + "page": 4, + "order": 107, + "type": "content" + }, + { + "text": "identifying potential interventions to manipulate birth SR, will be ", + "page": 4, + "order": 108, + "type": "content" + }, + { + "text": "critical to the effective preservation of genetic diversity in captive ", + "page": 4, + "order": 109, + "type": "content" + }, + { + "text": "breeding. ", + "page": 4, + "order": 110, + "type": "content" + }, + { + "text": "Supporting Information ", + "page": 4, + "order": 111, + "type": "content" + }, + { + "text": "Materials S1 ", + "page": 4, + "order": 112, + "type": "content" + }, + { + "text": "(DOCX) ", + "page": 4, + "order": 113, + "type": "content" + }, + { + "text": "5 ", + "page": 4, + "order": 114, + "type": "content" + }, + { + "text": " Mammalia", + "page": 4, + "order": 115, + "type": "content" + }, + { + "text": "Biased Birth Sex Ratios Lead to More Grandchildren ", + "page": 4, + "order": 116, + "type": "content" + }, + { + "text": " Z", + "page": 4, + "order": 117, + "type": "content" + }, + { + "text": "- ", + "page": 4, + "order": 118, + "type": "content" + }, + { + "text": "Variance in", + "page": 4, + "order": 119, + "type": "content" + }, + { + "text": "score SR ", + "page": 4, + "order": 120, + "type": "content" + }, + { + "text": "3.089 ", + "page": 4, + "order": 121, + "type": "content" + }, + { + "text": "4.197 ", + "page": 4, + "order": 122, + "type": "content" + }, + { + "text": "2.320 ", + "page": 4, + "order": 123, + "type": "content" + }, + { + "text": "2.061 ", + "page": 4, + "order": 124, + "type": "content" + }, + { + "text": "2.231 ", + "page": 4, + "order": 125, + "type": "content" + }, + { + "text": "4.880 ", + "page": 4, + "order": 126, + "type": "content" + }, + { + "text": "2.528 ", + "page": 4, + "order": 127, + "type": "content" + }, + { + "text": "2.821 ", + "page": 4, + "order": 128, + "type": "content" + }, + { + "text": "4.000 ", + "page": 4, + "order": 129, + "type": "content" + }, + { + "text": "2.024 ", + "page": 4, + "order": 130, + "type": "content" + }, + { + "text": "2", + "page": 4, + "order": 131, + "type": "content" + }, + { + "text": ") in F1 birth SR for granddams and grandsires ", + "page": 4, + "order": 132, + "type": "content" + }, + { + "text": " to enhance maternal and paternal fitness, ", + "page": 4, + "order": 133, + "type": "content" + }, + { + "text": " Mammalia", + "page": 4, + "order": 134, + "type": "content" + }, + { + "text": "July 2013 | Volume 8 | Issue 7 | e67867 ", + "page": 4, + "order": 135, + "type": "content" + }, + { + "text": "N ", + "page": 4, + "order": 136, + "type": "content" + }, + { + "text": "F ", + "page": 4, + "order": 137, + "type": "content" + }, + { + "text": "4 ", + "page": 4, + "order": 138, + "type": "content" + }, + { + "text": "3.560 ", + "page": 4, + "order": 139, + "type": "content" + }, + { + "text": "2 ", + "page": 4, + "order": 140, + "type": "content" + }, + { + "text": "4.838 ", + "page": 4, + "order": 141, + "type": "content" + }, + { + "text": "5 ", + "page": 4, + "order": 142, + "type": "content" + }, + { + "text": "2.674 ", + "page": 4, + "order": 143, + "type": "content" + }, + { + "text": "7 ", + "page": 4, + "order": 144, + "type": "content" + }, + { + "text": "2.376 ", + "page": 4, + "order": 145, + "type": "content" + }, + { + "text": "5 ", + "page": 4, + "order": 146, + "type": "content" + }, + { + "text": "2.572 ", + "page": 4, + "order": 147, + "type": "content" + }, + { + "text": "5 ", + "page": 4, + "order": 148, + "type": "content" + }, + { + "text": "4.777 ", + "page": 4, + "order": 149, + "type": "content" + }, + { + "text": "6 ", + "page": 4, + "order": 150, + "type": "content" + }, + { + "text": "2.475 ", + "page": 4, + "order": 151, + "type": "content" + }, + { + "text": "4 ", + "page": 4, + "order": 152, + "type": "content" + }, + { + "text": "2.761 ", + "page": 4, + "order": 153, + "type": "content" + }, + { + "text": "2 ", + "page": 4, + "order": 154, + "type": "content" + }, + { + "text": "3.916 ", + "page": 4, + "order": 155, + "type": "content" + }, + { + "text": "8 ", + "page": 4, + "order": 156, + "type": "content" + }, + { + "text": "1.982 ", + "page": 4, + "order": 157, + "type": "content" + }, + { + "text": ". Furthermore, our findings ", + "page": 4, + "order": 158, + "type": "content" + }, + { + "text": "P ", + "page": 4, + "order": 159, + "type": "content" + }, + { + "text": "0.0138 ", + "page": 4, + "order": 160, + "type": "content" + }, + { + "text": "0.0280 ", + "page": 4, + "order": 161, + "type": "content" + }, + { + "text": "0.0306 ", + "page": 4, + "order": 162, + "type": "content" + }, + { + "text": "0.0274 ", + "page": 4, + "order": 163, + "type": "content" + }, + { + "text": "0.0363 ", + "page": 4, + "order": 164, + "type": "content" + }, + { + "text": "0.0009 ", + "page": 4, + "order": 165, + "type": "content" + }, + { + "text": "0.0314 ", + "page": 4, + "order": 166, + "type": "content" + }, + { + "text": "0.0416 ", + "page": 4, + "order": 167, + "type": "content" + }, + { + "text": "0.0484 ", + "page": 4, + "order": 168, + "type": "content" + }, + { + "text": "0.0558 ", + "page": 4, + "order": 169, + "type": "content" + }, + { + "text": " versus", + "page": 4, + "order": 170, + "type": "content" + }, + { + "text": " granddams ", + "page": 4, + "order": 171, + "type": "content" + }, + { + "text": "Acknowledgments ", + "page": 5, + "order": 0, + "type": "content" + }, + { + "text": "We thank SDZG for access to their breeding records. Requests for data ", + "page": 5, + "order": 1, + "type": "content" + }, + { + "text": "should be directed to GAV at the SDZG. ", + "page": 5, + "order": 2, + "type": "content" + }, + { + "text": "References ", + "page": 5, + "order": 3, + "type": "content" + }, + { + "text": "1. Fisher RA (1930) The Genetical Theory of Natural Selection. Oxford: ", + "page": 5, + "order": 4, + "type": "content" + }, + { + "text": "Clarendon Press. ", + "page": 5, + "order": 5, + "type": "content" + }, + { + "text": "2. Hamilton WD (1967) Extraordinary sex ratios. A sex-ratio theory for sex linkage ", + "page": 5, + "order": 6, + "type": "content" + }, + { + "text": "and inbreeding has new implications in cytogenetics and entomology. Science ", + "page": 5, + "order": 7, + "type": "content" + }, + { + "text": "156: 477\u2013488. ", + "page": 5, + "order": 8, + "type": "content" + }, + { + "text": "3. West SA (2009) Sex allocation. Princeton: Princeton University Press. xii, 466 p. 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Cameron EZ (2004) Facultative adjustment of mammalian sex ratios in support ", + "page": 5, + "order": 23, + "type": "content" + }, + { + "text": "of the Trivers-Willard hypothesis: evidence for a mechanism. Proceedings of the ", + "page": 5, + "order": 24, + "type": "content" + }, + { + "text": "Royal Society of London Series B-Biological Sciences 271: 1723\u20131728. ", + "page": 5, + "order": 25, + "type": "content" + }, + { + "text": "11. Cockburn A, Legge S, Double MC (2002) Sex ratios in birds and mammals: can ", + "page": 5, + "order": 26, + "type": "content" + }, + { + "text": "the hypotheses be disentangled? In: Hardy ICW, editor. Sex ratios: concepts and ", + "page": 5, + "order": 27, + "type": "content" + }, + { + "text": "research methods. Cambridge: Cambridge University Press. 266\u2013286. ", + "page": 5, + "order": 28, + "type": "content" + }, + { + "text": "12. Gomendio M, Malo AF, Soler AJ, Fernandez-Santos MR, Esteso MC, et al. 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", + "page": 5, + "order": 37, + "type": "content" + }, + { + "text": "13. Cameron EZ, Dalerum F (2009) A Trivers-Willard effect in contemporary ", + "page": 5, + "order": 38, + "type": "content" + }, + { + "text": "14. Woodward M (1999) Epidemiology: study design and data analysis. Boca Raton, ", + "page": 5, + "order": 39, + "type": "content" + }, + { + "text": "15. Grafen A, Hails R (2002) Modern statistics for the life sciences. Oxford & New ", + "page": 5, + "order": 40, + "type": "content" + }, + { + "text": "16. Silk JB (1983) Local resource competition and facultative adjustment of sex- ", + "page": 5, + "order": 41, + "type": "content" + }, + { + "text": "17. Verme LJ, Ozoga JJ (1981) Sex-ratio of the white-tailed deer and the estrus ", + "page": 5, + "order": 42, + "type": "content" + }, + { + "text": "18. Catalano R, Bruckner T, Anderson E, Gould JB (2005) Fetal death sex ratios: a ", + "page": 5, + "order": 43, + "type": "content" + }, + { + "text": "19. Sheldon BC, West SA (2004) Maternal dominance, maternal condition, and ", + "page": 5, + "order": 44, + "type": "content" + }, + { + "text": "20. Cameron EZ, Linklater WL, Stafford KJ, Veltman CJ (1999) Birth sex ratios ", + "page": 5, + "order": 45, + "type": "content" + }, + { + "text": "21. Burke RL, Birch JM (1995) White-tailed deer vary offspring sex-ratio according ", + "page": 5, + "order": 46, + "type": "content" + }, + { + "text": "22. Weatherhead PJ, Robertson RJ (1979) Offspring Quality and the Polygyny ", + "page": 5, + "order": 47, + "type": "content" + }, + { + "text": "23. Faust LJ, Thompson SD (2000) Birth sex ratio in captive mammals: Patterns, ", + "page": 5, + "order": 48, + "type": "content" + }, + { + "text": "24. Glatston AR (1997) Sex ratio research in zoos and its implications for captive ", + "page": 5, + "order": 49, + "type": "content" + }, + { + "text": "6 ", + "page": 5, + "order": 50, + "type": "content" + }, + { + "text": "humans: male-biased sex ratios among billionaires. PLoS One 4: e4195. ", + "page": 5, + "order": 51, + "type": "content" + }, + { + "text": "FL: Chapman & Hall/CRC Press. ", + "page": 5, + "order": 52, + "type": "content" + }, + { + "text": "York: Oxford University Press. xv, 351 p. ", + "page": 5, + "order": 53, + "type": "content" + }, + { + "text": "ratios in relation to competitive abilities. American Naturalist 121: 56\u201366. ", + "page": 5, + "order": 54, + "type": "content" + }, + { + "text": "cycle. Journal of Wildlife Management 45: 710\u2013715. ", + "page": 5, + "order": 55, + "type": "content" + }, + { + "text": "test of the economic stress hypothesis. International Journal of Epidemiology 34: ", + "page": 5, + "order": 56, + "type": "content" + }, + { + "text": "944\u2013948. ", + "page": 5, + "order": 57, + "type": "content" + }, + { + "text": "offspring sex ratio in ungulate mammals. American Naturalist 163: 40\u201354. ", + "page": 5, + "order": 58, + "type": "content" + }, + { + "text": "relate to mare condition at conception in Kaimanawa horses. Behavioral ", + "page": 5, + "order": 59, + "type": "content" + }, + { + "text": "Ecology 10: 472\u2013475. ", + "page": 5, + "order": 60, + "type": "content" + }, + { + "text": "to maternal condition and age. Ecological Research 10: 351\u2013357. ", + "page": 5, + "order": 61, + "type": "content" + }, + { + "text": "Threshold: \u2018\u2018The Sexy Son Hypothesis\u2019\u2019. The American Naturalist 113: 201\u2013 ", + "page": 5, + "order": 62, + "type": "content" + }, + { + "text": "208. ", + "page": 5, + "order": 63, + "type": "content" + }, + { + "text": "biases, and the implications for management and conservation. Zoo Biology 19: ", + "page": 5, + "order": 64, + "type": "content" + }, + { + "text": "11\u201325. ", + "page": 5, + "order": 65, + "type": "content" + }, + { + "text": "management. Applied Animal Behaviour Science 51: 209\u2013216. ", + "page": 5, + "order": 66, + "type": "content" + }, + { + "text": "Biased Birth Sex Ratios Lead to More Grandchildren ", + "page": 5, + "order": 67, + "type": "content" + }, + { + "text": "July 2013 | Volume 8 | Issue 7 | e67867 ", + "page": 5, + "order": 68, + "type": "content" + } + ] + }, + "corrections": {}, + "tables": [] +} \ No newline at end of file diff --git a/brodie_code/output/reports/batch_summary_20241206_121315.json b/brodie_code/output/reports/batch_summary_20241206_121315.json new file mode 100644 index 00000000..4aa3326a --- /dev/null +++ b/brodie_code/output/reports/batch_summary_20241206_121315.json @@ -0,0 +1,20 @@ +{ + "1000_WinningTheGeneticLottery.pdf": { + "filename": "1000_WinningTheGeneticLottery.pdf", + "size_mb": 0.226318359375, + "status": "success", + "errors": [], + "warnings": [ + "No headings detected" + ], + "stats": { + "num_pages": 6, + "num_tables": 0, + "num_headings": 0, + "num_corrections": 0, + "processing_time": 0.02321314811706543 + }, + "ocr_applied": false, + "ocr_stats": {} + } +} \ No newline at end of file diff --git a/brodie_code/output/reports/batch_summary_20241206_121315.xlsx b/brodie_code/output/reports/batch_summary_20241206_121315.xlsx new file mode 100644 index 00000000..bc334478 Binary files /dev/null and b/brodie_code/output/reports/batch_summary_20241206_121315.xlsx differ diff --git a/brodie_code/requirements.txt b/brodie_code/requirements.txt index 672fd9fd..22a55054 100644 --- a/brodie_code/requirements.txt +++ b/brodie_code/requirements.txt @@ -1,4 +1,4 @@ -PyMuPDF==1.23.7 # For PDF processing +PyMuPDF==1.22.5 # For PDF processing numpy>=1.21.0 pandas>=1.3.0 pytesseract>=0.3.8 @@ -6,4 +6,5 @@ opencv-python>=4.5.0 Pillow>=8.0.0 pdf2image>=1.16.0 tqdm>=4.62.0 -pyyaml>=5.4.0 \ No newline at end of file +pyyaml>=5.4.0 +openpyxl>=3.0.0 diff --git a/brodie_code/src/.DS_Store b/brodie_code/src/.DS_Store index 41b0ea88..bb36df9a 100644 Binary files a/brodie_code/src/.DS_Store and b/brodie_code/src/.DS_Store differ diff --git a/brodie_code/src/__pycache__/batch.cpython-312.pyc b/brodie_code/src/__pycache__/batch.cpython-312.pyc deleted file mode 100644 index 913179f0..00000000 Binary files a/brodie_code/src/__pycache__/batch.cpython-312.pyc and /dev/null differ diff --git a/brodie_code/src/accessibility_checker/.DS_Store b/brodie_code/src/accessibility_checker/.DS_Store new file mode 100644 index 00000000..0d5c9134 Binary files /dev/null and b/brodie_code/src/accessibility_checker/.DS_Store differ diff --git a/brodie_code/src/accessibility_checker/__init__.py b/brodie_code/src/accessibility_checker/__init__.py new file mode 100644 index 00000000..457ffa6d --- /dev/null +++ b/brodie_code/src/accessibility_checker/__init__.py @@ -0,0 +1,21 @@ +from .core.document import AccessibilityDocumentProcessor +from .core.batch import BatchPDFProcessor +from .core.enhance import EnhancedAccessibilityChecker +from .ocr.processor import OCRProcessor +from .utils.retry import RetryHandler, RetryConfig, OCRError, ProcessingError, OCRTimeoutError +from .utils.config import OCRConfig + +__version__ = "0.1.0" + +__all__ = [ + 'AccessibilityDocumentProcessor', + 'BatchPDFProcessor', + 'EnhancedAccessibilityChecker', + 'OCRProcessor', + 'RetryHandler', + 'RetryConfig', + 'OCRError', + 'ProcessingError', + 'OCRTimeoutError', + 'OCRConfig', +] diff --git a/brodie_code/src/accessibility_checker/__pycache__/__init__.cpython-312.pyc b/brodie_code/src/accessibility_checker/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 00000000..f16eccc4 Binary files /dev/null and b/brodie_code/src/accessibility_checker/__pycache__/__init__.cpython-312.pyc differ diff --git a/brodie_code/src/accessibility_checker/core/.DS_Store b/brodie_code/src/accessibility_checker/core/.DS_Store new file mode 100644 index 00000000..877d5d7a Binary files /dev/null and b/brodie_code/src/accessibility_checker/core/.DS_Store differ diff --git a/brodie_code/src/accessibility_checker/core/__init__.py b/brodie_code/src/accessibility_checker/core/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/brodie_code/src/accessibility_checker/core/__pycache__/__init__.cpython-312.pyc b/brodie_code/src/accessibility_checker/core/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 00000000..9482078f Binary files /dev/null and b/brodie_code/src/accessibility_checker/core/__pycache__/__init__.cpython-312.pyc differ diff --git a/brodie_code/src/accessibility_checker/core/__pycache__/batch.cpython-312.pyc b/brodie_code/src/accessibility_checker/core/__pycache__/batch.cpython-312.pyc new file mode 100644 index 00000000..f79c1e85 Binary files /dev/null and b/brodie_code/src/accessibility_checker/core/__pycache__/batch.cpython-312.pyc differ diff --git a/brodie_code/src/accessibility_checker/core/__pycache__/document.cpython-312.pyc b/brodie_code/src/accessibility_checker/core/__pycache__/document.cpython-312.pyc new file mode 100644 index 00000000..3df8e56d Binary files /dev/null and b/brodie_code/src/accessibility_checker/core/__pycache__/document.cpython-312.pyc differ diff --git a/brodie_code/src/accessibility_checker/core/__pycache__/enhance.cpython-312.pyc b/brodie_code/src/accessibility_checker/core/__pycache__/enhance.cpython-312.pyc new file mode 100644 index 00000000..0c1fb655 Binary files /dev/null and b/brodie_code/src/accessibility_checker/core/__pycache__/enhance.cpython-312.pyc differ diff --git a/brodie_code/src/processor/batch.py b/brodie_code/src/accessibility_checker/core/batch.py similarity index 91% rename from brodie_code/src/processor/batch.py rename to brodie_code/src/accessibility_checker/core/batch.py index 1482467d..bfa7f257 100644 --- a/brodie_code/src/processor/batch.py +++ b/brodie_code/src/accessibility_checker/core/batch.py @@ -8,9 +8,9 @@ from typing import Dict, List, Optional import pandas as pd from tqdm import tqdm -from .accessibility import AccessibilityDocumentProcessor -from .ocr import OCRProcessor -from .retry import RetryHandler, OCRError, OCRTimeoutError +from ..core.document import AccessibilityDocumentProcessor # Changed from .accessibility +from ..ocr.processor import OCRProcessor +from ..utils.retry import RetryHandler, OCRError, OCRTimeoutError class BatchPDFProcessor: def __init__( @@ -88,6 +88,7 @@ def process_single_pdf(self, pdf_path: Path) -> Dict: 'ocr_stats': {} } + processor = None try: # Create output paths base_name = pdf_path.stem @@ -109,6 +110,14 @@ def process_single_pdf(self, pdf_path: Path) -> Dict: processor.detect_tables() processor.analyze_reading_order() + # Save the processed PDF + try: + processor.doc.save(str(processed_path)) + logging.info(f"Saved processed PDF to: {processed_path}") + except Exception as e: + stats['warnings'].append(f"Failed to save processed PDF: {str(e)}") + logging.warning(f"Could not save processed PDF for {pdf_path.name}: {str(e)}") + # Verify text with OCR if processor is available ocr_stats = {} if self.ocr_processor: @@ -138,7 +147,7 @@ def process_single_pdf(self, pdf_path: Path) -> Dict: 'num_pages': len(processor.doc), 'num_tables': len(processor.tables), 'num_headings': sum(1 for elem in processor.text_elements - if elem.heading_level is not None), + if elem.heading_level is not None), 'num_corrections': sum(len(corr) for corr in processor.corrections.values()), 'processing_time': time.time() - start_time } @@ -158,6 +167,14 @@ def process_single_pdf(self, pdf_path: Path) -> Dict: stats['errors'].append(str(e)) logging.error(f"Error processing {pdf_path.name}: {str(e)}") + finally: + # Clean up: close the document + if processor and processor.doc: + try: + processor.doc.close() + except Exception as e: + logging.error(f"Error closing document {pdf_path.name}: {str(e)}") + return stats def process_directory(self) -> pd.DataFrame: @@ -278,4 +295,4 @@ def main(): print(f"\nOutput files located in: {output_dir}") if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/brodie_code/src/processor/accessibility.py b/brodie_code/src/accessibility_checker/core/document.py similarity index 90% rename from brodie_code/src/processor/accessibility.py rename to brodie_code/src/accessibility_checker/core/document.py index 845c3db5..c7686fa7 100644 --- a/brodie_code/src/processor/accessibility.py +++ b/brodie_code/src/accessibility_checker/core/document.py @@ -18,8 +18,8 @@ from dataclasses import dataclass from PIL import Image from .enhance import EnhancedAccessibilityChecker -from .retry import RetryHandler, RetryConfig, ProcessingError, OCRError -from .ocr import OCRProcessor, OCRTimeoutError +from ..utils.retry import RetryHandler, RetryConfig, ProcessingError, OCRError +from ..ocr.processor import OCRProcessor, OCRTimeoutError # ============= Data Classes ============= @@ -367,6 +367,12 @@ def verify_text_with_ocr(self) -> Dict[int, Dict]: raise return results + + def add_text_tags(self): + for page in self.doc: + for element in [e for e in self.text_elements if e.page_num == page.number]: + rect = fitz.Rect(element.x, element.y, element.x + element.width, element.y + element.height) + page.insert_text(rect.tl, element.text, fontsize=element.font_size) # ... rest of your existing methods ... def extract_text_with_positions(self): @@ -376,21 +382,50 @@ def extract_text_with_positions(self): for block in blocks: if "lines" in block: + current_y = None + for line in block["lines"]: - for span in line["spans"]: + spans = line.get("spans", []) + if not spans: + continue + + # Reset position tracking for new line + last_x = None + + for span in spans: + # Calculate spacing + x0, y0, x1, y1 = span["bbox"] + if last_x is not None: + space_width = x0 - last_x + # Add space if gap is large enough + if space_width > span["size"] * 0.3: # Adjust threshold as needed + text = " " + span["text"] + else: + text = span["text"] + else: + text = span["text"] + + # Create text element element = TextElement( - text=span["text"], - x=span["bbox"][0], - y=span["bbox"][1], - width=span["bbox"][2] - span["bbox"][0], - height=span["bbox"][3] - span["bbox"][1], + text=text, + x=x0, + y=y0, + width=x1 - x0, + height=y1 - y0, font_size=span["size"], font_name=span["font"], is_bold="Bold" in span["font"], page_num=page_num ) self.text_elements.append(element) - + + # Update tracking + last_x = x1 + + # Add line break if moving to new line + if self.text_elements: + self.text_elements[-1].text += " " + def detect_headings(self): font_sizes = defaultdict(int) for element in self.text_elements: @@ -483,7 +518,7 @@ def analyze_reading_order(self): reading_order += 1 remaining = [te for te in page_elements - if te.heading_level is None and te.table_cell is None] + if te.heading_level is None and te.table_cell is None] column_threshold = 50 columns = defaultdict(list) @@ -508,7 +543,7 @@ def _find_closest_text_element(self, ocr_element: OCRElement, page_num: int) -> center_y = (y1 + y2) / 2 return min(page_elements, - key=lambda e: ((e.x + e.width/2 - center_x) ** 2 + + key=lambda e: ((e.x + e.width/2 - center_x) ** 2 + (e.y + e.height/2 - center_y) ** 2) ** 0.5) def _add_correction(self, page_num: int, text_element: TextElement, ocr_element: OCRElement): @@ -583,7 +618,7 @@ def _export_table_structures(self) -> List[Dict]: 'rowspan': cell.rowspan, 'bbox': (cell.x, cell.y, cell.x + cell.width, cell.y + cell.height) } for row in table.rows - for cell in row if cell and cell.col == cell.col] + for cell in row if cell and cell.col == cell.col] } for table in self.tables] # ============= Batch Processor ============= @@ -683,7 +718,26 @@ def process_single_pdf(self, pdf_path: Path) -> Dict: processor.detect_headings() processor.detect_tables() processor.analyze_reading_order() - + processor.add_text_tags() + + # Save the processed PDF + try: + processor.doc.save( + str(processed_path), + garbage=4, + deflate=True, + clean=True, + pretty=True, + linear=True, + ascii=False, + expand=True, # This expands all abbreviations/shortcuts in the PDF + copy_streams=True # This preserves existing content streams + ) + logging.info(f"Saved processed PDF to: {processed_path}") + except Exception as e: + stats['warnings'].append(f"Failed to save processed PDF: {str(e)}") + logging.warning(f"Could not save processed PDF for {pdf_path.name}: {str(e)}") + # OCR processing with validation if self.ocr_processor: try: @@ -803,4 +857,4 @@ def main(): raise if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/brodie_code/src/processor/enhance.py b/brodie_code/src/accessibility_checker/core/enhance.py similarity index 100% rename from brodie_code/src/processor/enhance.py rename to brodie_code/src/accessibility_checker/core/enhance.py diff --git a/brodie_code/src/accessibility_checker/ocr/.DS_Store b/brodie_code/src/accessibility_checker/ocr/.DS_Store new file mode 100644 index 00000000..8f372d6c Binary files /dev/null and b/brodie_code/src/accessibility_checker/ocr/.DS_Store differ diff --git a/brodie_code/src/accessibility_checker/ocr/__init__.py b/brodie_code/src/accessibility_checker/ocr/__init__.py new file mode 100644 index 00000000..e5a0fbfd --- /dev/null +++ b/brodie_code/src/accessibility_checker/ocr/__init__.py @@ -0,0 +1,3 @@ +from .processor import OCRProcessor, OCRResult + +__all__ = ['OCRProcessor', 'OCRResult'] diff --git a/brodie_code/src/accessibility_checker/ocr/__pycache__/__init__.cpython-312.pyc b/brodie_code/src/accessibility_checker/ocr/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 00000000..aa7d28fc Binary files /dev/null and b/brodie_code/src/accessibility_checker/ocr/__pycache__/__init__.cpython-312.pyc differ diff --git a/brodie_code/src/accessibility_checker/ocr/__pycache__/processor.cpython-312.pyc b/brodie_code/src/accessibility_checker/ocr/__pycache__/processor.cpython-312.pyc new file mode 100644 index 00000000..955ce4a0 Binary files /dev/null and b/brodie_code/src/accessibility_checker/ocr/__pycache__/processor.cpython-312.pyc differ diff --git a/brodie_code/src/processor/ocr.py b/brodie_code/src/accessibility_checker/ocr/processor.py similarity index 98% rename from brodie_code/src/processor/ocr.py rename to brodie_code/src/accessibility_checker/ocr/processor.py index 65c714a5..831d3959 100644 --- a/brodie_code/src/processor/ocr.py +++ b/brodie_code/src/accessibility_checker/ocr/processor.py @@ -5,9 +5,8 @@ import pytesseract import cv2 from dataclasses import dataclass - -from .retry import RetryHandler, OCRError, OCRTimeoutError -from .config import OCRConfig +from ..utils.retry import RetryHandler, OCRError, OCRTimeoutError +from ..utils.config import OCRConfig OCRElementType = Literal['text', 'equation', 'reference', 'table'] @@ -223,4 +222,4 @@ def _rotate_image(self, image: np.ndarray, angle: float) -> np.ndarray: flags=cv2.INTER_CUBIC, borderMode=cv2.BORDER_REPLICATE ) - return rotated \ No newline at end of file + return rotated diff --git a/brodie_code/src/accessibility_checker/utils/.DS_Store b/brodie_code/src/accessibility_checker/utils/.DS_Store new file mode 100644 index 00000000..e0c4e0d6 Binary files /dev/null and b/brodie_code/src/accessibility_checker/utils/.DS_Store differ diff --git a/brodie_code/src/accessibility_checker/utils/__init__.py b/brodie_code/src/accessibility_checker/utils/__init__.py new file mode 100644 index 00000000..e208848f --- /dev/null +++ b/brodie_code/src/accessibility_checker/utils/__init__.py @@ -0,0 +1,4 @@ +from .retry import RetryHandler, RetryConfig, OCRError, ProcessingError, OCRTimeoutError +from .config import OCRConfig + +__all__ = ['RetryHandler', 'RetryConfig', 'OCRError', 'ProcessingError', 'OCRTimeoutError', 'OCRConfig'] diff --git a/brodie_code/src/accessibility_checker/utils/__pycache__/__init__.cpython-312.pyc b/brodie_code/src/accessibility_checker/utils/__pycache__/__init__.cpython-312.pyc new file mode 100644 index 00000000..e997bfa7 Binary 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b/brodie_code/src/accessibility_checker/utils/config.py similarity index 100% rename from brodie_code/src/processor/config.py rename to brodie_code/src/accessibility_checker/utils/config.py diff --git a/brodie_code/src/processor/retry.py b/brodie_code/src/accessibility_checker/utils/retry.py similarity index 92% rename from brodie_code/src/processor/retry.py rename to brodie_code/src/accessibility_checker/utils/retry.py index 96b9256c..f57700c1 100644 --- a/brodie_code/src/processor/retry.py +++ b/brodie_code/src/accessibility_checker/utils/retry.py @@ -5,8 +5,8 @@ from datetime import datetime import random import numpy as np # Add this import -import fitz -from .enhance import EnhancedAccessibilityChecker +from ..core.enhance import EnhancedAccessibilityChecker +import fitz class RetryableError(Exception): """Base class for errors that should trigger a retry.""" @@ -149,12 +149,4 @@ def perform_ocr(self, image: np.ndarray) -> str: except Exception as e: raise OCRError(f"OCR failed: {str(e)}") -# Example usage -processor = EnhancedAccessibilityDocumentProcessor() -try: - result = processor.process_document("/Users/broderickschipp/accessibility_project/input/1000_WinningTheGeneticLottery.pdf") - print(f"Processing successful: {result}") - -except ProcessingError as e: - print(f"Processing failed after all retries: {str(e)}") \ No newline at end of file diff --git a/brodie_code/src/main.py b/brodie_code/src/main.py index 4f1d1784..fa6e9f12 100644 --- a/brodie_code/src/main.py +++ b/brodie_code/src/main.py @@ -1,19 +1,9 @@ from pathlib import Path -import argparse -import yaml import logging from datetime import datetime -import sys - -# Add the src directory to Python path -sys.path.append(str(Path(__file__).parent)) - -from processor.batch import BatchPDFProcessor -from processor.accessibility import AccessibilityDocumentProcessor -from processor.enhance import EnhancedAccessibilityChecker -from processor.retry import RetryHandler, RetryConfig, ProcessingError, OCRError, OCRTimeoutError -from processor.ocr import OCRProcessor -from processor.config import ConfigurationManager +import yaml +from accessibility_checker.core.batch import BatchPDFProcessor +from accessibility_checker.utils.config import ConfigurationManager def setup_logging(log_dir: Path) -> None: """Set up logging configuration.""" @@ -29,53 +19,12 @@ def setup_logging(log_dir: Path) -> None: ] ) -def parse_arguments(): - """Parse command line arguments.""" - parser = argparse.ArgumentParser(description='PDF Accessibility Checker') - - parser.add_argument( - '--input-dir', - type=str, - required=True, - help='Directory containing PDF files to process' - ) - - parser.add_argument( - '--output-dir', - type=str, - required=True, - help='Directory for output files and reports' - ) - - parser.add_argument( - '--config', - type=str, - default='config.yaml', - help='Path to configuration file' - ) - - parser.add_argument( - '--workers', - type=int, - help='Number of worker processes (overrides config file)' - ) - - parser.add_argument( - '--ocr-timeout', - type=int, - default=30, - help='Timeout in seconds for OCR processing' - ) - - return parser.parse_args() - def main(): - # Parse command line arguments - args = parse_arguments() - - # Create output directory structure - output_dir = Path(args.output_dir) - output_dir.mkdir(parents=True, exist_ok=True) + # Use project structure paths + project_dir = Path(__file__).parent.parent + input_dir = project_dir / "input" + output_dir = project_dir / "output" + config_file = project_dir / "config.yaml" # Set up logging log_dir = output_dir / "logs" @@ -84,59 +33,30 @@ def main(): try: # Load configuration - logging.info(f"Loading configuration from {args.config}") - config_manager = ConfigurationManager(args.config) + logging.info(f"Loading configuration from {config_file}") + config_manager = ConfigurationManager(str(config_file)) processing_config = config_manager.get_processing_config() - # Override max_workers if specified in command line arguments - if args.workers: - processing_config.max_workers = args.workers - - # Initialize processors with retry capability - retry_handler = RetryHandler(RetryConfig( - max_attempts=processing_config.retry_count, - base_delay=2.0, - max_delay=30.0, - jitter=True - )) - - # Initialize OCR processor with retry and timeout - ocr_processor = OCRProcessor( - config=processing_config.ocr_settings, - retry_handler=retry_handler, - timeout=30 - ) - - # Initialize batch processor with OCR capability + # Initialize batch processor processor = BatchPDFProcessor( - input_dir=args.input_dir, - output_dir=args.output_dir, - max_workers=processing_config.max_workers, - ocr_processor=ocr_processor, - retry_handler=retry_handler + input_dir=str(input_dir), + output_dir=str(output_dir), + max_workers=processing_config.max_workers ) # Process files - logging.info("Starting batch processing") summary_df = processor.process_directory() - # Print processing summary - success_count = sum(summary_df['status'] == 'success') - failed_count = sum(summary_df['status'] == 'failed') - ocr_count = sum(summary_df.get('ocr_applied', False)) - + # Print summary print("\nProcessing Summary:") print(f"Total files processed: {len(summary_df)}") - print(f"Successfully processed: {success_count}") - print(f"Failed: {failed_count}") - print(f"OCR applied: {ocr_count}") - print(f"\nOutput files located in: {args.output_dir}") - - logging.info("Processing completed successfully") + print(f"Successfully processed: {sum(summary_df['status'] == 'success')}") + print(f"Failed: {sum(summary_df['status'] == 'failed')}") + print(f"\nOutput files located in: {output_dir}") except Exception as e: logging.error(f"Error in main process: {str(e)}", exc_info=True) raise if __name__ == "__main__": - main() \ No newline at end of file + main() diff --git a/brodie_code/src/processor/__pycache__/accessibility.cpython-311.pyc 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a/brodie_code/src/processor/__pycache__/retry.cpython-311.pyc b/brodie_code/src/processor/__pycache__/retry.cpython-311.pyc deleted file mode 100644 index efb0065d..00000000 Binary files a/brodie_code/src/processor/__pycache__/retry.cpython-311.pyc and /dev/null differ diff --git a/brodie_code/src/processor/init.py b/brodie_code/src/processor/init.py deleted file mode 100644 index c40d4f87..00000000 --- a/brodie_code/src/processor/init.py +++ /dev/null @@ -1,4 +0,0 @@ -from .accessibility import AccessibilityDocumentProcessor -from .batch import BatchPDFProcessor -from .enhance import EnhancedAccessibilityChecker -from .retry import RetryHandler, RetryConfig \ No newline at end of file diff --git a/brodie_code/src/requirements.txt b/brodie_code/src/requirements.txt deleted file mode 100644 index 07d007d0..00000000 --- a/brodie_code/src/requirements.txt +++ /dev/null @@ -1,9 +0,0 @@ -PyMuPDF==1.22.3 -numpy==1.24.3 -pandas==2.0.3 -pytesseract==0.3.10 -opencv-python==4.8.1.78 -Pillow==10.0.0 -pdf2image==1.16.3 -tqdm==4.65.0 -pyyaml==6.0.1 \ No newline at end of file diff --git a/brodie_code/src/utils/__pycache__/config.cpython-311.pyc b/brodie_code/src/utils/__pycache__/config.cpython-311.pyc deleted file mode 100644 index 14906df2..00000000 Binary files a/brodie_code/src/utils/__pycache__/config.cpython-311.pyc and /dev/null differ diff --git a/brodie_code/src/utils/init.py b/brodie_code/src/utils/init.py deleted file mode 100644 index 1123d5d2..00000000 --- a/brodie_code/src/utils/init.py +++ /dev/null @@ -1 +0,0 @@ -from ..processor.config import ConfigurationManager \ No newline at end of file diff --git a/brodie_code/venv/.DS_Store b/brodie_code/venv/.DS_Store index 036b2c01..e5f3c9eb 100644 Binary files a/brodie_code/venv/.DS_Store and b/brodie_code/venv/.DS_Store differ diff --git a/brodie_code/venv/lib/.DS_Store b/brodie_code/venv/lib/.DS_Store index 73980bba..5af6e8bf 100644 Binary files a/brodie_code/venv/lib/.DS_Store and 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