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比特派钱包最新版本app下载|pigs

作者：比特派钱包最新版本app下载

2024-03-07 20:33:01

笨猪五国_百度百科

_百度百科网页新闻贴吧知道网盘图片视频地图文库资讯采购百科百度首页登录注册进入词条全站搜索帮助首页秒懂百科特色百科知识专题加入百科百科团队权威合作下载百科APP个人中心笨猪五国播报讨论上传视频欧洲五个主权债券信用评级低的经济体的贬称收藏查看我的收藏0有用+10笨猪五国 [3]（英语：PIIGS），也叫作“群猪五国”或者“欧猪五国”又或者“欧洲五猪”，是国际债券分析家、学者和国际经济界媒体对欧洲五个主权债券信用评级较低的经济体的贬称。笨猪五国最初称为欧猪四国 "PIGS", 其中" I "指意大利，后来加入了爱尔兰。 [1]欧猪五国，这是国际经济媒体对欧洲5个较弱经济体的贬称，对经济不景气、出现债务危机的葡萄牙（Portugal）、意大利（Italy）、爱尔兰（Ireland）、希腊（Greece）、西班牙（Spain），这五个欧洲国家因其英文国名首字母组合“PIIGS”类似英文单词“pigs”(猪)，故因此得名。 [2]特别指各国的主权债券市场，这些国家的公共赤字也都超过了3%。 2010年初，欧洲有很多人将希腊、葡萄牙、西班牙、意大利、爱尔兰五国的英文首字母连在一起，称为“笨猪五国”。中文名笨猪五国外文名PIIGS共同点国家公共赤字都超过3%名称由来“PIIGS”类似英文单词“pigs”产生时间20世纪90年代初起其他称谓五国联盟、戏称五猪国目录1历史沿革2最新变种3原因分析4五国概况5危险系数历史沿革播报编辑笨猪五国地理位置从20世纪90年代初开始，人们用“欧猪四国(PIGS)”来称呼葡萄牙、意大利、希腊和西班牙这四个南欧国家，这些国家有相似的文化传统、相近的地理位置。2007年，鉴于情况近似，又加入近年同样面对财政赤字的爱尔兰。由于新世纪金融危机的出现，该名词最早由《新闻周刊》的专栏作家Juliane Von Reppert-Bismarck于2008年7月7日发行的杂志上刊登的文章《为什么猪不能飞》（Why Pigs Can't Fly）使用，用于指代处于金融困境的上述几个国家。欧猪五国的GDP占欧元区GDP的13.2%（2013年数据）。最新变种播报编辑另一方面，最近匈牙利政府也语出惊人的表示，自身财政与希腊一样面临重大危机而引发全球股市恐慌，不过财经专家表示，说匈牙利像希腊一样发生严重的金融危机有些过份夸张，除了因匈牙利尚未加入欧元区外，匈牙利本身的财政状况其实好过笨猪五国。不过为了避免危机发生，国际货币组织已前往匈牙利进行调查。除了上述的国家外，经济学家也开始点出法国、比利时、奥地利这三个西欧国家其财政可能将步笨猪国家的后尘。斯洛文尼亚、塞浦路斯、马耳他及波兰的财政情况也一样并不乐观。原因分析播报编辑笨猪五国国旗(5张)南欧四国历史悠久，古希腊和罗马文明一直影响到今天的世界，西班牙和葡萄牙是大航海时代的急先锋，曾几何时，整个南美洲及大部分非洲，尽数落入西葡两国囊中。进入现代以后，尽管前进步伐落后于美英德法日，但总体还是沿着欧洲列车的轨道运行发展，而且幸运的是，他们既没有像二战的德、日一样被摧残成一片焦土，也没有经受苏东剧变的冲击，欧盟成立后，他们又顺理成章地成为第一批成员。其国民生活富足安逸，懒散休闲，生活质量高，贫富差距小。表面上看，公共债务债台高筑，GDP增长抵不上债务增长幅度，是造成四国经济危机的成因。实际上，经济结构不合理、公共开支巨大，财政长期性的入不敷出，以及周边欧元区国家对资金、技术及人才等要素的吸附作用，才是让他们变“笨猪”的深层次原因。除开旅游业以及衍生的相关服务业以外，南欧国家的产业经济结构单一，在传统的造船、汽车等工业已日渐萧条之下，新兴产业却几乎是白纸一张，因此，各国的政府财政预算，在年年见涨的公共开支及福利补贴之下，无疑就会捉襟见肘，只好采用拆东墙补西墙的举债方式来解决，如果国家能以正常的偿付方式支付利息，在东家不差钱的时候靠着拖欠着到期的本钱，一般情况下，倒也玩得转，但是遇着经济危机，大伙都差钱了，连债主们都削减开支的时候，受到冲击的必然是以吃喝玩乐为主的旅游业，后果就是以旅游业为支柱产业的国家现金流慢慢枯竭，加上资金聚群逐利的本能，本国的资金都在危机时刻一股脑地往北方的法兰克福方向跑，信用评级机构此时也来凑热闹，将这些个国家的信用等级下调一两个级别，让他们旧债还不了，新债借不到，家里的开支还不能断，就等着某一天整个国家的“破产”，于是，一只只任人宰割的“猪”便横空出世了。五国概况播报编辑欧猪五国的财务状况表（2012年数据）：国家国内生产总值GDP增长率政府预算收入政府预算支出赤字国际收支信用评级（标普）葡萄牙238,8801.398%108,600114,700-6,100-126,300BB意大利2,014,079-2.82%1,139,0001,203,000-64,000-57,940BBB+希腊303,065-4.535%132,400143,800-11,400-36,400CC西班牙1,493,513-0.147%1,660,0001,524,000-57.000-52,480BBB+爱尔兰203,892-1.041%93,840110,800-16,960-12,600BBB+单位：百万美元危险系数播报编辑此前，最令投资者担心、也是被认为爆发危机可能性最大的国家分别为葡萄牙、爱尔兰、意大利、希腊和西班牙。对于谁会成为下一个爆发主权债务危机的国家，知名信用评级机构标准普尔做出了暗示。　首个字母发音的是葡萄牙。根据标准普尔的预计，葡萄牙本年度的财政赤字可能等于该国年度国内生产总值(GDP)的80%以上，公共债务规模甚至可能在2011年前升至GDP的90%或以上。实际上，在本质上存在着与葡萄牙类似危险的欧元区国家同样存在。其中的葡、意、希三国，还因为公共赤字超过欧盟稳定公约所规定的3%的标准，而和德国、法国一同受到了欧盟的纠正警告。2009年12月16日晚间，国际评级机构标准普尔宣布，将希腊的长期主权信贷评级下调一档，从“A-”降为“BBB+”。标普同时警告说，如果希腊政府无法在短期内改善财政状况，有可能进一步降低希腊的主权信用评级。[6]不过除主权信用评级遭降的希腊之外，葡萄牙、爱尔兰及意大利的状况：欧元区各国财长11月7日讨论葡萄牙的情况时认为，葡设立的纠正措施足以按预定的时间将其赤字降到欧盟稳定公约的标准之内；爱尔兰央行总裁帕特里克·霍诺汉则在8日表示，爱尔兰未来数年中面临的债务负担将是“沉重但尚可控的”；而意大利新任政府更是于7日制定了一个缩减该国公共赤字的计划，并受到了欧盟各国财长的欢迎和肯定。新手上路成长任务编辑入门编辑规则本人编辑我有疑问内容质疑在线客服官方贴吧意见反馈投诉建议举报不良信息未通过词条申诉投诉侵权信息封禁查询与解封©2024 Baidu 使用百度前必读 | 百科协议 | 隐私政策 | 百度百科合作平台 | 京ICP证030173号京公网安备110000020000

PIGS - MBA智库百科

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1 什么是PIGS

2 PIGS的危险系数[5]

3 参考文献

[编辑] 什么是PIGS

　　PIGS是指南欧的葡萄牙（Portugal）、意大利（Italy）、希腊（Greece）和西班牙（Spain）这四个国家依照首字母的组合，也因英文Pigs的原因，有称作四小猪、小猪四国、欧猪四国。后来，连同爱尔兰（Ireland）被称为“PIIGS”

　　它们之所以得到这一绰号，是因为它们进退维谷，无力振兴经济。相比之下，其竞争者却敢于走向国外，既激活了出口，又创造了就业。如今，为了降低通胀率，德国等经济火热的地区计划调高利率，这样就更会窒碍PIGS本已疲弱的增长。

　　PIGS was a derogatory acronym used mostly in 2008 by some British and North American journalists in finance and economy to refer to four countries of southern Europe: Portugal, Italy, Greece, and Spain.[1] These Eurozone countries had mixed economic performance in the few years before 2008; [2] and while suffering from large current account deficits and high unemployment, little more could be said to put them together, besides their location in southern Europe.[3] More recently Ireland is sometimes added as an additional "I." (PIIGS)[4]

[编辑] PIGS的危险系数[5]

　　此前，最令投资者担心、也是被认为爆发危机可能性最大的国家分别为葡萄牙、爱尔兰、意大利、希腊和西班牙。对于谁会成为下一个爆发主权债务危机的国家，知名信用评级机构标准普尔做出了暗示。

　　首个字母发音的是葡萄牙。根据标准普尔的预计，葡萄牙本年度的财政赤字可能等于该国年度国内生产总值(GDP)的80%以上，公共债务规模甚至可能在2011年前升至GDP的90%或以上。实际上，在本质上存在着与葡萄牙类似危险的欧元区国家同样存在。其中的葡、意、希三国，还因为公共赤字超过欧盟稳定公约所规定的3%的标准，而和德国、法国一同受到了欧盟的纠正警告。

　　2009年12月16日晚间，国际评级机构标准普尔宣布，将希腊的长期主权信贷评级下调一档，从“A-”降为“BBB＋”。标普同时警告说，如果希腊政府无法在短期内改善财政状况，有可能进一步降低希腊的主权信用评级。[6]

　　不过至少从目前来看，除主权信用评级遭降的希腊之外，葡萄牙、爱尔兰及意大利的状况：欧元区各国财长11月7日讨论葡萄牙的情况时认为，葡设立的纠正措施足以按预定的时间将其赤字降到欧盟稳定公约的标准之内；爱尔兰央行总裁帕特里克·霍诺汉则在8日表示，爱尔兰未来数年中面临的债务负担将是“沉重但尚可控的”；而意大利新任政府更是于7日制定了一个缩减该国公共赤字的计划，并受到了欧盟各国财长的欢迎和肯定。

[编辑] 参考文献

↑ Why Pigs Can’t Fly

↑ "Ten years on, beware a porcine plot".The Economist.June 5,2008

↑ The ECB at ten: A decade in the sun.The Economist.June 5, 2008

↑ Reform failures may still kill off the euro

↑ “PIGS”危险系数较大全球“潜伏”新主权债务危机

↑ 一周之内希腊主权信用评级被第二次降级.中国新闻网.2009年12月18日

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评论(共4条)提示:评论内容为网友针对条目"PIGS"展开的讨论，与本站观点立场无关。

221.137.43.* 在 2010年1月6日 09:08 发表

北欧白人还真势利,看不起自己南边的穷亲戚

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61.140.226.* 在 2014年10月20日 19:40 发表

切你歧视东南亚国家不

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119.130.87.* 在 2016年6月24日 16:24 发表

221.137.43.* 在 2010年1月6日 09:08 发表

北欧白人还真势利,看不起自己南边的穷亲戚

你还蛮虚伪的嘛

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113.104.148.* 在 2017年6月4日 13:33 发表

犀鸠利

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Skip to contentSearchShopGamesPuzzlesActionFunny Fill-InVideosAmazing AnimalsWeird But True!Party AnimalsTry This!AnimalsMammalsBirdsPrehistoricReptilesAmphibiansInvertebratesFishExplore MoreMagazinehistoryScienceSpaceU.S. StatesWeird But True!SubscribemenuPlease be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.Please be respectful of copyright. Unauthorized use is prohibited.1 / 41 / 4Pigs are actually quite clean. The pig’s reputation as a filthy animal comes from its habit of rolling in mud to cool off. Pigs are actually quite clean. The pig’s reputation as a filthy animal comes from its habit of rolling in mud to cool off. Photograph by Ulrich Mueller, DreamstimeAnimalsMammalsPigDespite their reputation, pigs are not dirty animals. They’re actually quite clean. The pig’s reputation as a filthy animal comes from its habit of rolling in mud to cool off. Pigs that live in cool, covered environments stay very clean.Common Name: PigsScientific Name: SusDiet: OmnivorePigs are also known as hogs or swine. Male pigs of any age are called boars; female pigs are called sows. Pigs are found and raised all over the world, and provide valuable products to humans, including pork, lard, leather, glue, fertilizer, and a variety of medicines. Most pigs raised in the United States are classified as meat-type pigs, as they produce more lean meat than lard, a fat used in cooking.In the wild, pigs eat everything from leaves, roots, and fruit to rodents and small reptiles. In the United States, farm-raised pigs eat commercially made diets of mostly corn. In Europe, pigs eat barley-based diets. Pigs have sharp tusks that help them dig and fight. Farmers often take off the tusks to avoid injury to people and other pigs.Sows give birth to a litter of young called piglets. They usually nurse the piglets for three to five weeks. Piglets weaned off their mother’s milk are not called piglets but are referred to as shoats.National Geographic MapsPlease be respectful of copyright. Unauthorized use is prohibited.Piglets weigh about 2.5 pounds (1.1 kilograms) at birth, and usually double their weight in one week. Fully grown, pigs can grow to between 300 and 700 pounds (140 and 300 kilograms), and sometimes much more. Pigs have poor eyesight, but a great sense of smell. The pig’s nostrils are on its leathery snout, which is very sensitive to touch. The pig uses the snout to search, or root, for food.Pigs are among the smartest of all domesticated animals and are even smarter than dogs.0:56Chris P. Bacon's WheelsChris P. Bacon the pig doesn't have use of his hind legs--so the critter gets around on sets of wheels. Check out a video of the unstoppable animal with his pig-mobiles.Explore more!Amazing AnimalsWatch to discover interesting facts about animals from all over the world.Comeback crittersSee how animal species in trouble have come back from the brink of extinction.Save the Earth tipsFind out how you can help make a difference.Endangered Species ActHow this 1973 law protects animalsLegalTerms of UsePrivacy PolicyYour California Privacy RightsChildren's Online Privacy PolicyInterest-Based AdsAbout Nielsen MeasurementDo Not Sell My InfoOur SitesNational GeographicNational Geographic EducationShop Nat GeoCustomer ServiceJoin UsSubscribeManage Your Subscription Copyright © 1996-2015 National Geographic SocietyCopyright © 2015-2024 National Geographic Partners, LLC. All rights reserved

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Pigs, Hogs & Boars: Facts About Swine

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By Alina Bradford, Scott Dutfield published 5 October 2018

From piglets to sows and sounder, discover the lives of one of Earth's most recognisable animals

(Image credit: Getty Images)

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Conservation status

Pigs are members of the Suidae family, which includes eight genera and 16 species. Among those species are wild boars, warthogs, pygmy hogs and domestic pigs. Archaeological evidence suggests that pigs were domesticated around 10,500 years ago in the Near East, before farmers first brought them to Europe around 8,500 years ago, according to research published in the journal Proceedings of the National Academy of Sciences. Domestic pigs are descended mainly from the wild boar (Sus scrofa) and the Sulawesi warty pig (Sus celebensis), diverging from their closest ancestors about 500,000 years ago according to the Encyclopedia of Life. Currently there are approximately 752 million domestic pigs worldwide, 406 million of which can be found in China, according to Statista. Related story: Warty pig is oldest animal cave art on recordHow big are pigs?Pigs usually weigh between 300 and 700 lbs. (140 and 300 kilograms), but domestic pigs are often bred to be heavier. The largest pig in history was a swine called Big Bill, who stood at 5 feet (1.52m) tall and weighed an impressive 2,552 lbs (1,157 kilograms), according to Guinness World Records. Wild pigs on the other hand vary greatly in size and weight. The largest boar is the giant forest hog (Hylochoerus meinertzhageni). Native to more than a dozen countries across Africa, it grows up to 6.6 feet (2 meters) long and measures 3.6 feet (1.1 metres) tall, according to the Encyclopedia of Life. Though it is rarely seen, video of the elusive beast was captured in June 2018 by ecologists in Uganda, National Geographic reported.The heaviest boar is the Eurasian wild pig (Sus scrofa), which grows to 710 lbs. (320 kg), and the smallest boar is the pygmy hog (Sus salvanius). This delicate swine grows to a length between 1.8 and 2.4 feet (55 to 71 centimeters) and stands 9.8 inches (25 cm) tall from hoof to shoulder. The pygmy hog only weighs 14.5 to 21 lbs. (6.6 to 9.7 kg), according to the San Diego Zoo.Where do boars live?Boars, pigs and hogs live all over the world, except for Antarctica, northern Africa and far northern Eurasia, according to the Encyclopedia of Life. For example, red river hogs (Potamochoerus porcus), also called bush pigs, are found in Africa; babirusas (Babyrousa babyrussa), or pig deer, are found in Indonesia; and Visayan warty pigs (Sus cebifrons) come from the Philippines. Wild pigs typically live in grasslands, wetlands, rain forests, savannas, scrublands and temperate forests. Whenever they have the chance, all pigs wallow in mud as it helps them to regulate their body temperature and discourages parasites.Swine behaviour Pigs are very intelligent animals. According to a review published in 2015 in the International Journal of Comparative Psychology, pigs are "cognitively complex," sharing many traits with animals that are typically considered to be highly intelligent. The review analyzed findings from a number of studies, suggesting that pigs were capable of remembering objects, perceiving time, and making use of learned information to navigate their environment. Pigs are also playful and have a wide range of play behaviors — another indication of intelligence in animals, the researchers reported.In 2020, researchers at Pennsylvania State University put pig intelligence to the test in a series of joystick-operated video tasks. Two Panepinto micro pigs and two Yorkshire pigs (Sus scrofa) were trained to control the movements of the computer cursor via a joystick, a test used to assess the cognitive abilities of other animals, such as monkeys and pigeons. The pigs were tasked with making contact between the cursor and a randomly placed target on the screen. On successful contact an automatic dispenser released a food pellet reward. All pigs were "significantly above chance on first attempts to contact one-walled target", the authors of the study wrote. This suggests that these pigs were able to make the association between the joystick and the cursor.They are also very social. Feral pigs often travel in close-knit groups called sounders, which typically consist of two females and their young, according to Texas Parks and Wildlife.Pigs communicate with a variety of grunts and squeaks. A short grunt, a longer growl and a loud roar will warn other pigs of approaching danger, according to the San Diego Zoo. The pigs' primary defense is speed, but when cornered, their tusks can be formidable weapons. Their lower tusks can get to be about 3 inches long (7 cm) and are razor sharp.Related: Pigs can breathe through their butts. Can humans?What do pigs eat?Pigs, boars and hogs are omnivores and will eat just about anything. Wild boars, for example, fill the majority of their diet with roots, seeds, bulbs and green plants, according to the Woodland Trust, however as opportunistic feeders they will also chow down on invertebrates, carrion (decaying flesh) and even small mammals found on the forest floor. Domestic pigs and hogs are fed feed that is made from corn, wheat, soy or barley. On small farms, pigs are often fed "slop," which consists of vegetable peels, fruit rinds and other leftover food items. Most species of pigs process plants in their hindguts; however, their digestion of cellulose is inefficient, requiring them to feed often, according to the Encyclopedia of Life.How many offspring do pigs have?Domestic pigs can breed throughout the year without any seasonal constraints. Once pregnant, female pigs, commonly called sows, carry a litter of around 10 piglets for approximately 114 days before giving birth, according to the animal welfare organisation Compassion in World Farming. Within the first six hours piglets suckle the "first milk", also known as colostrum, which is jam-packed with nutrients and essential antibodies to build the piglet's immune system. If the piglet drinks the first milk after 25 hours of being born their intestines will not be able to successfully absorb the antibodies in the milk, according to the Agriculture and Horticulture Development Board. Wild pigs mate during the winter season, when solitary males seek out a potential mate. Once impregnated, wild sows will also give birth to around 10 piglets and will share the responsibility of raising them until they reach 1 year old. At which point the sounder will return to his solitary life-style, according to the Woodland Trust. Conservation statusWild boars are not endangered, according to the International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species. They are listed as "least concern" due to the wild pig's "wide range, abundance, tolerance to habitat disturbance and presence in many protected areas."Related: FDA approves genetically engineered pigs for food and transplantsHistorically wild boar have been driven to extinction in various countries around the world, for example in England by 1260, boar had been hunted to complete eradication, Countryside has previously reported. However, through introduction programmes there are currently over 4,000 wild boar throughout the United Kingdom, BBC Countryfile has previously reported. Although wild boar populations are generally not considered endangered, there are several species under threat. Sulawesi warty pigs (Sus celebensis) and Palawan bearded pigs (Sus ahoenobarbus) are listed as "near threatened"; Philippine warty pigs (Sus philippensis) are "vulnerable"; Javan warty pigs (Sus verrucosus) are "endangered"; and Visayan warty pigs are "critically endangered." Hunting and habitat loss are cited as the causes of declining populations in these species, according to the IUCN. Additional resources:

Discover different breeds of pigs with The Illustrated Guide to Pigs by Celia Lewis

Learn more about the origins of pigs by reading The Pig: A Natural History by Richard Lutwyche

For more information about pig farming head to The Countryside Charity

This article was updated on Oct. 5, 2018 by Live Science Senior Writer, Mindy Weisberger. Editor's Note: This article was updated at 4:16 PM EDT on Oct. 10, 2018 to reflect a correction. A previous version incorrectly stated that pigs are not found in Australia.

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Alina BradfordSocial Links NavigationLive Science ContributorAlina Bradford is a contributing writer for Live Science. Over the past 16 years, Alina has covered everything from Ebola to androids while writing health, science and tech articles for major publications. She has multiple health, safety and lifesaving certifications from Oklahoma State University. Alina's goal in life is to try as many experiences as possible. To date, she has been a volunteer firefighter, a dispatcher, substitute teacher, artist, janitor, children's book author, pizza maker, event coordinator and much more.

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Pigs - Facts, Information & Farm Pictures

- Facts, Information & Farm Pictures Animal CornerDiscover the many amazing animals that live on our planet.HomeA-Z AnimalsAnatomyGlossaryAnimal ListsAnimal By LetterAnimals by LocationMammalsBirdsReptilesAmphibiansSpirit AnimalsFree ResourcesAnimal Coloring PagesAnimal JokesAnimal QuizzesPetsDog BreedsRabbit BreedsCat BreedsPet RodentsAnimal CareBlogYou are here: Home / Animals / PigsPigsImage SourceThe pig was domesticated approximately 5,000 to 7,000 years ago and are found across most of the world including Europe, the Middle East and into Asia as far as Indonesia and Japan. They are one of the oldest forms of livestock, and were domesticated earlier than cows. Nowadays, pigs are farmed for their meat widely around the globe, although some keep them as pets.Pigs belong to the genus ‘Sus‘, within which there are 11 extant and many extinct species. The domestic pig ‘Sus domesticus‘ is by some accounts considered to be a subspecies of the wild boar ‘Sus scrofa’ but by other accounts is a species of its own. The latter is the general consensus, but to be fair the differences can be slight.The genus Sus, along with one other ‘Porcula’ are the only extant genera within the tribe ‘Suini‘, which is part of the family ‘Suidae‘. There is only one species of domestic pig, but there are many wild pigs and many breeds within the species.ChartacteristicsThe distinction between wild and domestic animals is slight and domestic pigs have become feral (A feral animal or plant is one that has escaped from domestication and returned, partly or wholly, to its wild state) in many parts of the world (for example, New Zealand) and caused substantial environmental damage.Many people who know pigs compare them to dogs because they are friendly, loyal and intelligent. Pigs are naturally very clean and avoid, if at all possible, soiling their living areas. When given the chance to live away from factory farms, pigs will spend hours playing, lying in the sun and exploring their surroundings with their powerful sense of smell. Pigs are very clever animals.BehaviourPigs are known to be intelligent animals and have been found to be more trainable than dogs or cats. Asian pot-bellied pigs, a smaller subspecies of the domestic pig, have made popular house pets in many countries.Regular domestic farmyard pigs have also been known to be kept indoors, however, due to their large size and destructive tendencies, they typically need to be moved into an outdoor pen as they grow older. Most pigs also have an extreme fear of being picked up, however, they will usually calm down once placed back on the floor.DietPigs are naturally omnivores, meaning they eat both plants and animals. However, many domestic pigs are fed mostly plant and vegetables but this does vary by country. Here’s a peek into what pigs munch on:In the Wild, Pigs have a varied diet consisting of leaves, roots, fruits, rodents, and small reptiles.On the Farm – In the United States, farm-raised pigs usually eat commercially made diets primarily composed of corn, while in Europe, they often consume barley-based diets.Pig BreedsThere are 14 different breeds of pig within the United Kingdom and many more other different pig breeds throughout the world. UK breeds are divided into two groups, ‘Traditional pigs’ and ‘Modern pigs’.Traditional pig breeds include: Berkshire, Hampshire, Large Black, Large White, Middle White, Tamworth Pigs, Wessex Saddleback, Chester White, Gloucester Old Spots, Oxford Sandy and Black, British Lop and the Welsh pig.The Modern pigs include: The Duroc Pig and the Landrace Pig.Interesting Facts About PigsA group of pigs is called a herd.The scientific name for the pig is sus scrofa domesticusPigs walk on only two of their toes on each feet. Pigs look like they are walking on tip toe..Pigs do not have sweat glands and white pigs burn easily in the sun, hence having to roll in mud to keep cool..Pigs are not dirty animals – they tend to soil a particular part of their pen, away from eating and sleeping areas..Scientists believe that pigs are one of the most intelligent animals, ranking close behind apes and dolphins.Pigs are distantly related to the hippopotamus family.The word ‘barbecue’ comes from the French who called their Caribbean pork feasts ‘de barbe et queue’, which means ‘from beard to tail’.Wild or domestic pigs can be found on every continent except Antarctica.There are approximately 840 million hogs on farms throughout the world.China has long had the world’s largest population of domestic pigs.The average sow gives birth to 8 to 12 pigs at a time.Duroc pigs are a popular breed because they produce large litters and gain weight rapidly.Cincinnati, Ohio was such a major pork processing centre by 1863 that is was widely known as ‘porkapolis’.Pigs do not need to be rounded up. A good yell will bring them running.A pig’s squeal can reach up to 115 decibels, 3 decibels higher than the sound of a supersonic Concorde.Improved genetics and better feeding practices have resulted in a market hog 50% leaner than it was in the 1960’s.An average pig eats five pounds of feed each day, or a ton of food every year.The largest pig on record was a Poland-China hog named ‘Big Bill’. He weighed a portly 2,552 lbs and was so large that he dragged his belly on the ground. He had a shoulder height of 5 feet and a length of 9 feet.The smallest breed of pig is the Mini Maialino. Pigs of this breed average only 20 pounds at maturity.The largest litter of piglets ever farrowed was 37 by a sow on a farm in Australia. 36 piglets were born alive and 33 total survived.The largest piglet ever farrowed was a stillborn 5lb 4oz male. Average weight for a piglet is 3 lbs.What is the Scientific Name for a pig?The scientific name for the pig is sus scrofa domesticus.More Fascinating Animals to Learn AboutDomestic PigAnimals by GroupAnimals by Endangered StatusGuinea PigsTeira Batfish (Platax teira)Animals Beginning with CAbout Joanne SpencerI've always been passionate about animals which led me to a career in training and behaviour. As an animal professional I'm committed to improving relationships between people and animals to bring them more happiness.Animal ClassificationKingdom:AnimaliaPhylum:ChordataClass:MammaliaOrder:ArtiodactylaFamily:SuidaeGenus:SusSpecies:S. domesticusBinomial name:Sus domesticusSearchMost Popular AnimalsZebras Aquatic Warbler Atlantic DolphinsTrapdoor SpiderGiraffe MeerkatsTimber WolfPraying MantisHuntsman SpiderVampire Bat Animal Names Glossary Mammals Dog Breeds Farm Animals Best of the BlogFreshwater Marvels – 21 Awesome Animals that Live in LakesWhat are the Fastest Animals in the World?31 Animals with Funny Names and Weird Sounding Names: Humor in NatureTop 15 Deadliest Animals in the World – The Most Fatal Creatures You May EncounterOphiophagy – Examples of animals that eat snakesList of Fascinating Solitary AnimalsCopyright © 2005-2024 · Animal Corner · All Rights Reserved · Affiliate Disclaimer · Privacy Policy · Animals Sitemap . About Us AnimalCorner.org is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com. Amazon and the Amazon logo are trademarks of Amazon.com, Inc. or its affiliates.

Pigs - The Domestication History of Sus Scrofa

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The Domestication of Pigs: Sus Scrofa's Two Distinct Histories

How did the wild boar become the sweet domestic pig?

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K. Kris Hirst

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Updated on July 03, 2019

The domestication history of pigs (Sus scrofa) is a bit of an archaeological puzzle, in part because of the nature of the wild boar that our modern pigs are descended from. Many species of wild hog exist in the world today, such as the warthog (Phacochoreus africanus), the pygmy hog (Porcula salvania), and the pig-deer (Babyrousa babyrussa); but of all the suid forms, only Sus scrofa (wild boar) has been domesticated.

That process took place independently about 9,000-10,000 years ago in two locations: eastern Anatolia and central China. After that initial domestication, pigs accompanied early farmers as they spread out of Anatolia to Europe, and out of central China to the hinterlands.

All of the modern swine breeds today — there are hundreds of breeds around the globe — are considered forms of Sus scrofa domestica, and there is evidence that the genetic diversity is decreasing as cross-breeding of commercial lines threatens indigenous breeds. Some countries have recognized the issue and are beginning to support the continued maintenance of the non-commercial breeds as a genetic resource for the future.

Distinguishing Domestic and Wild Pigs

It must be said that it is not easy to distinguish between wild and domestic animals in the archaeological record. Since the early 20th century, researchers have segregated pigs based on the size of their tusks (lower third molar): wild boars typically have broader and longer tusks than domestic pigs. Overall body size (in particular, measures of knucklebones [astralagi], front leg bones [humeri] and shoulder bones [scapulae]) has been commonly used to differentiate between domestic and wild pigs since the mid-twentieth century. But wild boar body size alters with climate: hotter, drier climates mean smaller pigs, not necessarily less wild ones. And there are notable variations in body size and tusk size, among both wild and domestic pig populations even today.

Other methods used by researchers to identify domesticated pigs include population demography — the theory is that pigs kept in captivity would have been slaughtered at younger ages as a management strategy, and that can be reflected in the ages of the pigs in an archaeological assemblage. The study of Linear Enamel Hypoplasia (LEH) measures the growth rings in tooth enamel: domestic animals are more likely to experience stress episodes in diet and those stresses are reflected in those growth rings. Stable isotope analysis and tooth wear can also give clues to the diet of a particular set of animals because domestic animals are more likely to have had grain in their diets. The most conclusive evidence is genetic data, which can give indications of ancient lineages.

See Rowley-Conwy and colleagues (2012) for a detailed description of the benefits and pitfalls of each of these methods. In the end, all a researcher can do is look at all of these available characteristics and make her best judgment.

Independent Domestication Events

Despite the difficulties, most scholars are agreed that there were two separate domestication events from geographically separated versions of the wild boar (Sus scrofa). Evidence for both locations suggest that the process began with local hunter-gatherers hunting wild boars, then over a period of time began managing them, and then purposefully or unconsciously keeping those animals with smaller brains and bodies and sweeter dispositions.

In southwest Asia, pigs were part of a suite of plants and animals that were developed in the upper reaches of the Euphrates river about 10,000 years ago. The earliest domestic pigs in Anatolia are found in the same sites as domestic cattle, in what is today southwestern Turkey, about 7500 calendar years BC (cal BC), during the late Early Pre-Pottery Neolithic B period.

Sus Scrofa in China

In China, the earliest domesticated pigs date to 6600 cal BC, at the Neolithic Jiahu site. Jiahu is in east-central China between the Yellow and Yangtze Rivers; domestic pigs were found associated with the Cishan/Peiligang culture (6600-6200 cal BC): in Jiahu's earlier layers, only wild boars are in evidence.

Beginning with the first domestication, pigs became the main domestic animal in China. Pig sacrifice and pig-human interments are in evidence by the mid-6th millennium BC. The modern Mandarin character for "home" or "family" consists of a pig in a house; the earliest representation of this character was found inscribed on a bronze pot dated to the Shang period (1600-1100 BC).

Pig domestication in China was a steady progress of animal refinement lasting a period of some 5,000 years. The earliest domesticated pigs were primarily herded and fed millet and protein; by the Han dynasty, most pigs were raised in small pens by households and fed millet and household scraps. Genetic studies of Chinese pigs suggest an interruption of this long progress occurred during the Longshan period (3000-1900 BC) when pig burials and sacrifices ceased, and previously more or less uniform pig herds became infused with small, idiosyncratic (wild) pigs. Cucchi and colleagues (2016) suggest this may have been the result of a social-political change during the Longshan, although they recommended additional studies.

The early enclosures used by Chinese farmers made the process of pig domestication much faster in China compared to the process used on western Asian pigs, which were allowed to roam freely in European forests up through the late Middle Ages.

Pigs Into Europe

Beginning about 7,000 years ago, central Asian people moved into Europe, bringing their suite of domestic animals and plants with them, following at least two main paths. The people who brought the animals and plants into Europe are known collectively as the Linearbandkeramik (or LBK) culture.

For decades, scholars researched and debated whether Mesolithic hunters in Europe had developed domestic pigs prior to the LBK migration. Today, scholars mostly agree that European pig domestication was a mixed and complex process, with Mesolithic hunter-gatherers and LBK farmers interacting at different levels.

Soon after the arrival of LBK pigs in Europe, they interbred with the local wild boar. This process, known as retrogression (meaning successful interbreeding of domesticated and wild animals), produced the European domestic pig, which then spread out from Europe, and, in many places replaced the domesticated Near Eastern swine.

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Cucchi T, Hulme-Beaman A, Yuan J, and Dobney K. 2011. Early Neolithic pig domestication at Jiahu, Henan Province, China: clues from molar shape analyses using geometric morphometric approaches. Journal of Archaeological Science 38(1):11-22.

Cucchi T, Dai L, Balasse M, Zhao C, Gao J, Hu Y, Yuan J, and Vigne J-D. 2016. Social complexification and pig (Sus scrofa) Husbandry in ancient China: A combined geometric morphometric andiIsotopic approach. PLOS ONE 11(7):e0158523.

Evin A, Cucchi T, Cardini A, Strand Vidarsdottir U, Larson G, and Dobney K. 2013. The long and winding road: identifying pig domestication through molar size and shape. Journal of Archaeological Science 40(1):735-743.

Groenen MAM. 2016. A decade of pig genome sequencing: a window on pig domestication and evolution. Genetics Selection Evolution 48(1):1-9.

Krause-Kyora B, Makarewicz C, Evin A, Girdland Flink L, Dobney K, Larson G, Hartz S, Schreiber S, Von Carnap-Bornheim C, Von Wurmb-Schwark N et al. 2013. Use of domestic pigs by Mesolithic hunter-gatherers in northwestern Europe. Nature Communications 4(2348).

Larson G, Liu R, Zhao X, Yuan J, Fuller D, Barton L, Dobney K, Fan Q, Gu Z, Liu X-H et al. 2010. Patterns of East Asian pig domestication, migration, and turnover revealed by modern and ancient DNA. Proceedings of the National Academy of Sciences 107(17):7686-7691.

Lega C, Raia P, Rook L, and Fulgione D. 2016. Size matters: A comparative analysis of pig domestication. The Holocene 26(2):327-332.

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Origin and dispersal of early domestic pigs in northern China

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Origin and dispersal of early domestic pigs in northern China

Hai Xiang1,2, Jianqiang Gao3, Dawei Cai4, Yunbing Luo5, Baoquan Yu6, Langqing Liu1, Ranran Liu7, Hui Zhou4, Xiaoyong Chen8, Weitao Dun8, Xi Wang9, Michael Hofreiter10 & …Xingbo Zhao1 Show authors

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AbstractIt is widely accepted that modern pigs were domesticated independently at least twice, and Chinese native pigs are deemed as direct descendants of the first domesticated pigs in the corresponding domestication centers. By analyzing mitochondrial DNA sequences of an extensive sample set spanning 10,000 years, we find that the earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Our data set also supports early Neolithic pig utilization and a long-term in situ origin for northeastern Chinese pigs during 8,000–3,500 BP, suggesting a possibly independent domestication in northeast China. Additionally, we observe a genetic replacement in ancient northeast Chinese pigs since 3,500 BP. The results not only provide increasing evidence for pig origin in the middle Yellow River region but also depict an outline for the process of early pig domestication in northeast China.

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04 January 2024

Takahiro Yonezawa, Hideyuki Mannen, … Yoshio Yamamoto

IntroductionIt is widely accepted that pigs were domesticated independently in Near East and East Asia beginning ~10,000 years ago after Sus sp. emerged in Southeast Asia during the climatic fluctuations of the early Pliocene 5.3–3.5 My ago1,2,3. So far, at least six phylogeographically distinct wild boar lineages have been found to have contributed to the present domestic pig populations4. Over the past decade, regions in China, including the Mekong River basin5, the downstream region of the Yangtze River5, the upper stream region of the Yangtze River6, the Tibetan highlands7 and the lower region of the Yellow River8, 9 have been suggested as regions from which wild boar have contributed to the domestic pig gene pool and which may have represented independent centers for pig domestication.Zoo-archaeological studies on the pig remains from the Early Neolithic assemblages in China back this idea of multiregional pig domestication in East Asia. The faunal assemblages of the ~9,000-y-old Zhenpiyan cave site10 in Guangxi province and the ~8,000-y-old Kuahuqiao site11 in Zhejiang Province both provide evidence for a commensal domestication phase12 in the Mekong River basin and the downstream region of Yangtze River. Furthermore, numerous pig remains excavated in the ~10,500-y-old Nanzhuangtou site13, the ~9,000-y-old Jiahu site14, and the ~7,500-y-old Cishan site15 as well as palaeogenetic studies8 presented the middle and lower branches of the Yellow River as one of the earliest regions for pig domestication. Extensive archaeological findings in these regions, such as broomcorn millet, foxtail millet, dog and chicken, are evidence for early origins of mixed agriculture16,17,18. Besides the archaeological findings, pigs seem to have had cultural significance for the communities in this region because two pig skeletons were buried with humans at Xinglongwa Site (8,200–7,400 BP), implying either that pigs may already have been domesticated in Northeast China around 8,000 years ago or that wild boar had cultural significance19, 20.It has previously been shown that, at least with regard to maternal lineages, Chinese native pig breeds were direct descendants of the first domesticated pigs in the corresponding geographical regions8, 9. However, it is likely that roaming in a semi-managed status during the beginning of domestication allowed recurrent genetic exchange between domesticated pigs and indigenous wild boars. Thus, even during the beginning of domestication, genetic similarity between domestic pigs and wild boar from the same region may indicate introgression of wild boar haplotypes into the domestic gene pool rather than independent domestication events. Moreover, human migrations and cultural expansions repeatedly took place in East Asia during the past 10,000 years. Thus, human-mediated dispersal of and gene flow among domestic pig populations would not have been uncommon. Both for European and Near Eastern pigs, ancient DNA and dental geometric morphometric analyses have revealed nonlinear patterns of early domestication, dispersal of animals, genetic turnover and interaction among various geographic regions21,22,23.We have collected pig remains from 15 archaeological sites in China, including Jiahu and another two of the oldest archaeological sites in the middle Yellow River basin (Nanzhuangtou and Cishan), three sites in Northeast China (Xinglongwa, Wanfabozi and Dashanqian), and one site (Changning) in the upper region of the Yellow River. We investigated partial mitochondrial DNA control region (CR) sequences and a segment of the cytochrome b gene (Cytb) from both ancient and modern pigs, aiming to uncover the pattern of early maternal domestication and lineage dispersal in China. Locations and details for all samples can be found in Fig. 1 and Table S1.Figure 1Locations of samples. The orange dots depict all sites from which we retrieved ancient pig sequences. The inset shows the location of the region within China. The maps are modified from free map materials deposited in the public database of National Administration of Surveying, Mapping and Geoinformation (http://219.238.166.215/mcp/index.asp).Full size image

ResultsUsing loop-mediated PCR (L-PCR) followed by a specific singleplex PCR (for primers used see Table S2), we retrieved 49 Cytb fragments (Table S3) and 15 CR fragments (Table S4) of ancient pig samples from 15 archaeological sites. By combining our new results with previously reported sequences, we obtained a data set of 38 ancient pig CR sequences from China (Table S4) and combined Cytb/CR sequences from 37 samples, ranging geographically from northeast to northwest China and temporally from 10,000 BP to 2,500 BP (Table S1). We confirmed the Neolithic context of some of the early samples by determining the ages of the archaeological pig bones by direct radiocarbon dating of two bones from Cishan site, one bone from Nanzhuangtou site and one bone from Xinglongwa site. These samples yielded calibrated dates of ∼7,600, ∼7,800, ∼10,500 and ∼7,500 years, respectively (Tables S1 and S5), confirming the archaeologically determined ages.We aligned the 37 combined sequences with 97 published homologous sequences of extant wild boar, native pig breeds and commercial pig breeds from all over the world (Table S6). Phylogenetic analyses resulted in two apparent clusters, which represent Asian and European origins, respectively (Fig. 2). All 10,000 BP to 2,500 BP Chinese pigs were found in the Asian clade (Fig. 2).Figure 2Bayesian consensus phylogenetic tree of the 37 combined (Cytb and control region) ancient pig sequences and 98 extant published homologous sequences. Ages (modern vs. ancient), status (wild vs. domestic) and geographical origin are depicted in different colours (see bottom left of the figure). The European and Asian sequence clusters are framed.Full size image

To investigate the source of the genetic diversity in Asian pigs in more detail, we compared ancient and modern Asian pigs based on the mitochondrial Cytb sequences alone. We aligned our 49 ancient sequences (Table S3) with 506 extant homologous sequences, which represent modern Asian pigs deposited in GenBank (Table S7). We found 20 SNPs among all Asian pig sequences, which constituted 21 haplotypes (Table S7). The 20 SNPs included 10 nonsynonymous substitutions, by which we classified Asian pigs into 11 groups defined by different Cytb amino acid sequences. The group AA1 contained 10 haplotypes representing 525 sequences (almost 95% of the sequences) and all geographically defined pig types from Asia (Fig. 3a and b), making this haplogroup the predominant haplogroup among Asian pigs. The groups AA2-AA11 contained the remaining 30 sequences, representing pigs from China, Japan, Korea and South East Asia Island, with one to maximally two AA substitutions to AA1 in this region of Cytb (Fig. 3a and b, Table S7) with various Grantham conservative scores24, 25.Figure 3Ancient Cytb gene analyses. Relationship of pig Cytb amino acid sequences. (a) Each haplogroup is represented by a circle, with the area of the circle proportional to the haplogroup’s frequency. Different colors indicate samples originating from different regions. The numbers alongside AA changes are the Grantham scores which help classify the conservation levels of AA changes. The number of asterisks highlights the level: non - considered conservative; one - moderately conservative; two - moderately radical and three - radical, respectively. (b) Alignment of AA changes among the 11 AA haplogroups and 21 DNA haplotypes. The AA haplogroups and DNA haplotypes containing ancient pigs are in red font.Full size image

The 38 ancient CR sequences obtained (Table S4) were aligned with 1,716 published homologous sequences from China, including 1,495 modern native domestic pigs and 221 wild boar (Table S8), representing 73 haplotypes (Table S8). Using the warthog (P. africanus) as outgroup, the consensus Bayesian tree resulted in three clades and a large polytomy representing the majority of the sequences (Fig. S1). The largest one (in red) of the three clades consisted of 8 haplotypes representing 12 Tibet Plateau pig samples and 1 haplotype representing 1 wild boar and 1 domestic pig each from southwest China. The other two clades (in green) were formed only by wild boars, in which one contained 2 haplotypes (representing 9 sequences) and the other one contained 3 haplotypes (25 sequences). The polytomy consisted of numerous branches, where three haplotypes were found only in ancient samples, 21 haplotypes were found only in wild boar, and 20 haplotypes only in modern domestic pigs, 6 of which were found only in Plateau pigs, while the remaining nine haplotypes were found in wild boars, ancient samples and modern domestic pigs (Table S8).The 38 CR sequences obtained from ancient samples constitute 11 haplotypes (Table 1 and Fig. S2). Haplotypes H2 and H3 first appeared in Nanzhuangtou samples from the middle Yellow River valley in northern China at least 10,500 BP (~10,000 yrs for H2 from the indirectly dated dNZT1-3 sample and, ~10,500 yrs for H3 from the directly dated sample dNZT4). We also found haplotype H3 in sample dJH1 from Jiahu dated to ~9,000 BP. Haplotype H4 was first found in sample dJH2 also from Jiahu dating to at least ~8,500 BP. We also found it in sample dCS2 from Cishan (directly dated to ~7,800 yrs), and at Xinglongwa in Northeast China dating to 7,400–8,000 BP (sample dXLW1). The ancient sample dXLW2 from Xinglongwa, directly dated to ~7,500 BP, yielded haplotype H18, which also appeared in sample dWD2 from Wadian in the middle Yellow River area dating to ~4,000 BP. The ancient sample dCS1 from Cishan, directly dated to ~7,600 yrs, yielded haplotype H19 which also emerged in sample dWD3 from Wadian (~4,000 BP). We also found five rare haplotypes amongst our ancient samples. Two younger samples from Northeast China were identified as the rare haplotypes H31 (sample dWBP1 from Wanfabozi, 5,000–4,000 BP) and H70 (sample dDSQ2 from Dashanqian, 4,000–3,500 BP), while three ~4,000-y-old samples from the middle Yellow River region, dWD1, dGCJ1 and dGCJ3, yielded the rare haplotypes H71, H72 and H73, respectively. Except for those samples carrying rare haplotypes, ancient samples younger than 4,500 yrs carried haplotype H10 or haplotypes H2, H3 and H4 that were already found in the oldest samples (Table 1 and Fig. S2).Table 1 Haplotype composition of ancient samples for control region sequences.Full size table

Together, the four haplotypes H2, H3, H4 and H10 accounted for 1,376 of the 1,754 investigated sequences (almost 80%), clearly representing the dominant haplotypes found in Chinese pigs (Table 1 and Fig. S3). Moreover, haplotypes that appeared before 7,000 BP in the middle Yellow River valley, including the dominant haplotypes H2, H3 and H4 as well as the less dominant haplotype H19, were repeatedly found in different historical sites, and represent a large part of the haplotypic diversity found in modern Chinese pigs (~55% of modern pigs carry these haplotypes; Fig. 4 and Table 1). In contrast, the fourth dominant haplotype, H10, which is found in ~25% of modern Chinese pigs, was detected only around 4,500 years ago in several sites across China within our data set (Fig. 4 and Table 1). Other contemporaneous haplotypes H70, H72 and H73 were generally detected almost exclusively in ancient pigs, except H70, which we found in one modern pig (Table 1). These three rare haplotypes are genetically close to the dominant haplotypes H2 or H10, separated by only one or two SNPs. A similar picture arises in Northeast China, where the ~4,000 y old haplotypes H31 and H71 were found, which are close to H2 and H10, respectively. While we did not find H71 in modern pigs, H31 interestingly appeared in two modern wild populations (Table S8). Moreover, the 8,000–7,400 years old remains in Northeast China carried not only the dominant haplotype H4 but also the less dominant haplotype H18. Even though H18 was never found in modern samples from Northeast China, it was detected in a younger sample (4,000 BP) from Wadian from the middle Yellow River region and at ~2.4% in modern pig populations in southern China (Fig. 4 and Table 1). Finally, for the ~4,000 year old samples from the upper region of the Yellow River and the middle region of the Yangtze River, we found that they shared similar haplotype compositions with ancient pigs in the middle Yellow River basin (Fig. 4). Overall, after their first appearance in the middle region of the Yellow River and Northeast China, most of the oldest haplotypes were inherited into younger times up to modern Chinese pigs (Fig. 4 and Table 1).Figure 4Temporal transition of mtDNA control region haplotypes of ancient Chinese pigs in different regions. The upper left map shows the location of the investigated region within China. From left to right and top to bottom: Time series of maps identifying the locations and haplotypes of ancient pig samples from which DNA sequences were obtained. Each symbol corresponds to a single sample. Different colours indicate different haplotypes (see lower right panel of the figure). The pie chart at the lower right shows the proportions of the different haplotypes in present day Chinese pigs. Maps are modified from free map materials deposited in the public database of National Administration of Surveying, Mapping and Geoinformation (http://219.238.166.215/mcp/index.asp).Full size image

DiscussionIt is generally accepted that pigs were domesticated in at least two separate domestication centers, Europe and Asia26,27,28. In our data set of mitochondrial DNA sequences from ancient Chinese pigs, we found both considerable differences in haplotype composition over time and long-term continuity of some haplotypes.The middle Yellow River basin has long been discussed as one center for early Chinese pig domestication based on both ancient DNA and morphometric evidence8, 14, 29. Already the earliest pig remains from this region revealed the haplotypes that represent the dominant maternal lineages in modern Chinese pigs (Table 1), supporting the hypothesis that the middle Yellow River basin indeed was one of the earliest centers for pig domestication from where domestic pigs spread to other regions in China. In a previous study, we demonstrated maternal lineage continuity in pigs from between ~9,000-y-old remains in the middle and ~4,000-y-old ones in the upper region of the Yellow River9. The present results from two samples from Changning in the upper region of the Yellow River further support this interpretation. Moreover, isotope data from Dadiwan in the upper Yellow River region provided evidence for a cultural replacement by central Chinese Neolithic cultures before 4,000 BP30, suggesting a possible reason why the ~4,000 BP pigs in the upper Yellow River region could have originated from progenitors from the middle Yellow River region. Similar to our previous study9, additional samples from Qinglongquan in the middle Yangtze River region also carry the dominant haplotypes that were already found in ~10,000 BP samples from the middle Yellow River drainage, suggesting a possible southward migration before (or around) ~4,000 year ago.Due to close relationships between humans and pigs and evidence of early millet farming at Xinglongwa, Northeast China has been proposed as another region of early pig domestication20. However, only pig remains younger than 8,000 BP are assumed to represent domesticated ones19. In the present study, Xinglongwa specimens carry the dominant modern haplotype H4 and the less common haplotype H18, respectively, demonstrating maternal continuity between the earliest archaeological pig remains in this region and modern Chinese domestic pigs (Fig. 4 and Table 1). The haplotype H4 also appears in Jiahu and Cishan around the same time (Fig. 4), suggesting either early population migrations, trade of early domestic pigs or parallel domestication across the North China Plain and Northeast China. Suidae remains in Xinglongwa were found in all three cultural phases (8,200–8,000 BP, 8,000–7,400 BP and 7,400–7,000 BP)19, suggesting continuous utilization of pigs during the early Neolithic in this region. The younger haplotypes H31 and H71 discovered in Northeast China (Wanfabozi and Dashanqian) have so far not been found in the middle Yellow River region (Fig. 4 and Table 1), implying also long-term in situ continuity after initial pig domestication, or possibly, introgression of wild boar haplotypes into imported, early domestic pig herds, in Northeast China.In addition to long-term continuity, we also observed genetic turnovers in ancient Northeast Chinese pigs. One example is haplotype H18, which we found in a ~7,500 year old sample from Xinglongwa, but which seems to have disappeared afterwards in Northeast China. However, we found it in younger samples from the middle Yellow River region ~4,000 BP (Fig. 4 and Table 1) and also in modern pigs from southern China. In contrast, the rare haplotype H71, which we found in a single ~3,500 year old sample from Northeast China has not yet been found in modern pigs (Table 1), indicating that genetic drift also played a role in the history of domestic pigs during the last 3,500 BP. This view is further supported by haplotypes H72 and H73, which are both from the ~4,000 BP Guchengzhai site in the middle Yellow River Region and have not been found in any younger sites or modern pigs so far.The last pattern was found for haplotype H31 (Table S7), which we discovered only in one 4,000–5,000 year old sample from Northeast China and in two wild boar from southern China. In contrast to past pig populations, modern pigs in Northeast China show a similar mitochondrial haplotype composition as other regions (Fig. S3 and Table S7), suggesting extensive homogenization of pig populations over time, accompanied by a loss of at least some of the original, regional maternal lineages.ConclusionOur results support early independent domestication and long-term genetic continuity of pigs both in Europe and East Asia. The earliest pigs from the middle Yellow River region already carried the maternal lineages that are dominant in both younger archaeological populations and modern Chinese pigs. Moreover, there is strong evidence for early Neolithic pig utilization and possibly independent domestication, or alternatively, incorporation of local wild boar into introduced domestic pig populations in northeast China. However, this in situ origin for northeastern Chinese pigs ended around 3,500 BP due to genetic replacement, likely by pigs originating from the middle Yellow River region.Materials and MethodsSample InformationWe used ninety-three ancient pig specimens (bones or teeth) for DNA analyses, which originate from 15 archaeological sites in northern and central China (Fig. 1), including 65 specimens from nine sites in the lower and middle area of the Yellow River drainage basin (Nanzhuangtou and Cishan sites in Hebei province; Jiahu, Nanwa, Guchengzhai, Wadian and Wangchenggang sites in Henan province; Taosi and Gaohong sites in Shanxi province), 6 specimens from two sites located in the upper region of the Yellow River (Lajia and Changning sites in Qinghai province), 12 specimens from one site (Qinglongquan site in Hubei province) located in the middle region of the Yangtze River, and 10 specimens from three sites in Northeast China (Xinglongwa and Dashanqian sites in eastern Inner Mongolia and Wangfabozi site in Jilin province). Dates of these archaeological sites ranged from 10,600 to 2,500 years before present. Details regarding the archaeological sites and the contexts from which the specimens were recovered can be found in Table S1.Sample Preparation and Ancient DNA ExtractionAll pre-PCR work was conducted in the Ancient DNA Laboratory at China Agricultural University. Samples were prepared by cautiously cleaning the adhering soils and other external contaminations using abrasive paper, and then washing them with 5% (vol/vol) sodium hypochlorite solution followed by double-distilled water and drying under UV-irradiation. After that, bones and teeth were ground to fine-grained powder.DNA was extracted by using the QIAamp DNA Investigator kit (Qiagen) and Amicon Ultra-4 filters (Millipore). DNA extraction followed the QIAamp DNA Investigator handbook for purification of total DNA from bones or teeth. Amicon Ultra-4 (Millipore, 10 K) filters were used to concentrate ancient DNA to a final volume of ∼50 μL. Several mock extractions were carried out alongside the samples in the same manner to monitor for contamination.Amplification and Sequencing of Ancient DNAWe used loop-mediated PCR (L-PCR) followed by a specific singleplex PCR amplification and Sanger sequencing to obtain the targeted ancient pig DNA sequences. As previously described18, L-PCR is designed to efficiently enrich the target copy number using loop-mediated isothermal amplification primer sets; subsequent singleplex PCR then allows generating a specific amplicon that can then be sequenced.Primers were designed according to the published mitochondrial sequence of S. scrofa (NC_000845). All L-PCR primers were designed by online loop-mediated isothermal amplification primer designing software (primerexplorer.jp/e/). The primer set of the mitochondrial Cytb gene was newly designed for this study. The L-PCR primer pair of the mitochondrial control region was designed based on the control region PCR primer pair described by Larson et al.8. Amplicons of the Cytb gene and the control region were 101 bp and 138 bp in size, respectively, and contained polymorphic sites which were used to define haplogroups or haplotypes. Detailed primer sequences are available in Table S2.L-PCR and the specific singleplex PCR amplification were setup as previously described18. Several blank controls were performed in all PCR assays. L-PCR used the following cycling conditions: 37 °C for 10 min, 94 °C for 5 min, followed by 35 cycles of 94 °C for 30 s, 65 °C for 40 s, 72 °C for 30 s, and a final extension of 10 min at 72 °C. Secondary PCR used the following cycling conditions: 37 °C for 10 min, 94 °C for 5 min, followed by 35 cycles of 94 °C for 30 s, 61 °C for 30 s, 72 °C for 30 s, and a final extension of 10 min at 72 °C. Amplifications of the extraction blank controls and PCR blank controls were performed in all experiments to monitor contaminations. Amplification success was controlled by electrophoresis on a 2% agarose gel. Subsequently, PCR products were purified using the QIAquick PCR purification kit (Qiagen). Sequencing was carried out on an ABI 3730XL automated DNA sequencer (Applied Biosystems) using the ABI Prism Big Dye Terminator v3.1 Cycle Sequencing kit.Independent Replication ExperimentsFor all ancient DNA samples, we performed several replication experiments in the Ancient DNA Laboratory at China Agricultural University. Moreover, some of the positive samples were sent to the Ancient DNA Laboratory at the Research Center for Chinese Frontier Archeology at Jilin University for independent replication experiments (Table S1). DNA extraction, amplification and sequencing were carried out using the same methods and conditions in both laboratories.Radiocarbon Dating AnalysisAll samples used in the present study were from well-defined archaeological contexts. Nevertheless, four ancient bones from the three key archaeological sites of Nanzhuangtou (1 bone), Cishan (2 bones) and Xinglongwa sites (1 bone), which yielded DNA sequences were sent for radiocarbon dating using direct accelerator mass spectrometry at Beta Analytic Inc. (USA) to provide further support of their ages (Table S5).Data AnalysesThe reconstructed ancient DNA sequences were aligned with extant published homologous sequences from wild boars, local domestic pigs and commercial breeds from all over the world (Table S6). The ancient Cytb gene sequences (Table S3) and homologous sequences of Asian S. scrofa were aligned and investigated considering both DNA and amino acid (AA) phylogenetic relationship (Table S7). Particularly, to determine the origin and dispersal pattern of the dominant haplotypes in Chinese pig breeds, the ancient control region sequences (Table S4) were utilized in comparison with published sequences of ancient and modern Chinese domestic pigs and wild boars (Table S8). Sequences were aligned using MUSCLE31 or the online tool MAFFT32, and edited using MEGA 633; then the online tool FaBox (users-birc.au.dk/biopv/php/fabox/) was used to classify haplotypes34. MrBayes 3.2.335 was used for phylogenetic analysis with model parameters identified by jModelTest 2.1.136. The length of the MCMC was set to 10,000,000. Parameter estimates and consensus trees resulting from 10 MrBayes runs were recorded and compared. The best supported phylogenetic consensus tree was summarized with discarding the first 25% as burn-in. The tree was depicted using the software FigTree v1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). Median-joining networks37 were reconstructed using the software Network 4.6.1.0 (www.fluxus-engineering.com/index.htm). The aligned DNA sequence file format conversions were performed using BioEdit 7.038 and Forcon 1.039.

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Download referencesAcknowledgementsWe express great thanks to Prof. Jing Yuan (Institute of Archaeology, Chinese Academy of Social Science) for generously helping ancient sample collection, Prof. Dengyun Qiao (Handan Municipal Institute of Cultural Relics and Archaeology) and Associated Prof. Xue Ling (Northwest University) for discussions and comments, Dr. Jikun Wang and Dr. Tao Yin (China Agricultural University) for experimental assistance, and Dr. Ye Zhang (Jilin University) for replication experiments. This work was funded by the National Natural Science Foundation of China (31672379), the National Key Basic Research Program of China (2014CB138500) and the China Postdoctoral Science Foundation (2015M581201).Author informationAuthors and AffiliationsNational Engineering Laboratory for Animal Breeding; Ministry of Agricultural Key Laboratory of Animal Genetics, Breeding and Reproduction; and College of Animal Science and Technology, China Agricultural University, Beijing, 100193, ChinaHai Xiang, Langqing Liu & Xingbo ZhaoInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, ChinaHai XiangHebei Provincial Institute of Cultural Relic, Shijiazhuang, 050031, ChinaJianqiang GaoAncient DNA Laboratory, Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, 130023, ChinaDawei Cai & Hui ZhouHubei Provincial Institute of Cultural Relics and Archaeology, Wuhan, 430077, ChinaYunbing LuoXushui County Office for Preservation of Ancient Monuments, Xushui, 072550, ChinaBaoquan YuInstitute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, ChinaRanran LiuInstitute of Animal Science and Veterinary of Hebei Province, Baoding, 071000, ChinaXiaoyong Chen & Weitao DunInstitute of Animal Science and Veterinary Medicine, Shanxi Academy of Agricultural Science, Taiyuan, 030032, ChinaXi WangFaculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, GermanyMichael HofreiterAuthorsHai XiangView author publicationsYou can also search for this author in

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PubMed Google ScholarContributionsX.Z. designed research; H.X., D.C., R.L., L.L., H.Z., X.C., W.D. and X.W. performed research; J.G., D.C., Y.L. and B.Y. contributed new reagents/analytic tools; H.X., L.L., M.H. and X.Z. analyzed data; and H.X., M.H., and X.Z. interpreted the data and wrote the paper.Corresponding authorsCorrespondence to

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Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs | Scientific Reports

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Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs

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Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs

Xiong Tong1,3 na1, Lianjie Hou1 na1, Weiming He

ORCID: orcid.org/0000-0003-0483-53902, Chugang Mei4, Bo Huang1, Chi Zhang2, Chingyuan Hu5 & …Chong Wang1 Show authors

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AbstractChinese indigenous pigs exhibit considerable phenotypic diversity, but their population structure and the genetic basis of agriculturally important traits need further exploration. Here, we sequenced the whole genomes of 24 individual pigs representing 22 breeds distributed throughout China. For comparison with European and commercial breeds (one pig per breed), we included seven published pig genomes with our new genomes for analyses. Our results showed that breeds grouped together based on morphological classifications are not necessarily more genetically similar to each other than to breeds from other groups. We found that genetic material from European pigs likely introgressed into five Chinese breeds. We have identified two new subpopulations of domestic pigs that encompass morphology-based criteria in China. The Southern Chinese subpopulation comprises the classical South Chinese Type and part of the Central China Type. In contrast, the Northern Chinese subpopulation comprises the North China Type, the Lower Yangtze River Basin Type, the Southwest Type, the Plateau Type, and the remainder of the Central China Type. Eight haplotypes and two recombination sites were identified within a conserved 40.09 Mb linkage-disequilibrium (LD) block on the X chromosome. Potential candidate genes (LEPR, FANCC, COL1A1, and PCCA) influencing body size were identified. Our findings provide insights into the phylogeny of Chinese indigenous pig breeds and benefit gene mining efforts to improve major economic traits.

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IntroductionApproximately 10,000 years ago, pigs (Sus scrofa L.) were independently domesticated in multiple Eurasian regions1,2. China is a major center of early pig domestication3 and therefore has numerous indigenous breeds that exhibit considerable phenotypic variation in response to both artificial and natural selection. Except for wild boars, Chinese indigenous pigs are historically classified into 48 breeds and split into six types (South Chinese, North China, Lower Yangtze River Basin, Central China, Southwest, and Plateau), based on geographic distribution, historical origin, and morphological characteristics4. Some molecular evidences5,6,7,8 suggests that this classification may be problematic, given the potential for admixture among different types. However, these studies used a small number of molecular markers, including randomly amplified polymorphic DNA5 and microsatellites6,7,8, and therefore this admixture has not been well studied yet.With the development of genome sequencing and SNP chip technologies, the past decade has seen an increase in data on genome-wide variation. Indeed, comparative genomic analyses have identified genes involved in a wide range of agriculturally-important traits, including coat color9,10, body size11,12,13, meat yield11, and disease resistance11. DNA-based techniques provide an excellent opportunity to clarify the Chinese pig classification. Recent studies investigated only a few breeds with highly desirable production-related traits10,13, and focused on identifying selective sweeps during domestication14,15. Such research included genome-wide analyses of domestic breeds (e.g., Tibetan14, Tongcheng10, Enshi Black13, and Rongchang16) with a focus on tolerance to harsh environments, high fertility, and body size. Currently, too few Chinese pig breeds have been studied to provide a conclusive investigation of porcine evolution in China. Specific loci and genes underlying common phenotypic variation among Chinese domestic pig breeds have not yet been studied.To address these deficiencies, we performed whole-genome resequencing of pigs representing 22 breeds distributed across different geographical areas in China. This new sequence data was integrated with publically-available sequence data from seven other pig breeds, including European breeds. We uncovered population genetic structures among Chinese indigenous pigs, genetic introgression between population pairs (North China, South China, and Europe), LD patterns of X-chromosome, along with potential candidate genes associated with body size.Results and discussionSequencing and variation identificationTwenty-four animals representing twenty-two pig breeds were individually resequenced (Table 1 and Supplementary Fig. S1 and Table S1). The average effective sequencing depth was 17.54 (±7.30)×, and genomic coverage was 94.74 (±0.69)% (Supplementary Fig. S2 and Table S2).Table 1 Summary of the sample information.Full size tableTo these data, we included genomic data12,17 publically available for seven pigs of wild and commercial European and Chinese breeds (Table 1). The combined dataset had 14.09 billion high-quality raw reads (1,281.12 Gb raw bases, >90% Q30 bases) (Supplementary Fig. S3).A strict quality-filter pipeline resulted in 19,685,697 single-nucleotide polymorphisms (SNPs) from 31 pigs (Supplementary Table S3). Of these SNPs, 13,430,360 (68.22%) were in intergenic regions, 1,223,834 (6.22%) were 5-Kb upstream or downstream of gene regions, and 5,031,503 (25.56%) were within gene regions. The last group contained 46,618 non-synonymous (NS) and 53,028 synonymous (S) SNPs (Supplementary Fig. S4), leading to an NS/S ratio (ω) of 0.88, which is higher than the ratio of 0.68 reported by Li et al.14. This study collected more local pig breeds in China than Li et al.14, resulting in a higher NS/S ratio. In this study, 20 Chinese domestic pig breeds covering the whole country were collected. In the study of Li et al.14, although the number of individuals reached 45, only Tibetan pigs and five other local Chinese breeds distributed in Sichuan and Chongqing were collected.In addition, we identified 5,081,752 small-to-medium (1–20 bp) indels (Supplementary Table S4). As expected, most indels (3,486,145, 68.60%) occurred in intergenic regions; the remainder were either 5 Kb upstream or downstream of gene regions (352,227, 6.93%), or in gene regions (1,243,380, 24.47%). The Frameshift/Non-frameshift ratio was 2.24 (Supplementary Fig. S5). Larger structural variations (SV, >45 bp) were detected using read-pair and read-depth methods. Across individuals, the SV count varied from 2,881 to 49,939. Deletions and intra-chromosomal translocations were the two primary SV types identified in our samples (Supplementary Table S5).Homozygous (Hom) and heterozygous (Het) SNPs were classified per individual. Homozygous SNPs were more common in all European pigs than in Chinese pigs, especially in two European wild boars that had Hom/Het SNP ratios of 3.804–4.460 (Supplementary Table S3). Furthermore, except for the Large White (LW) pig, higher Hom/Het ratios of indels were observed in European pigs than in Chinese pigs, which was consistent with that of SNP variants (Supplementary Table S4). These results suggest that population bottlenecks may be responsible for the reduced genetic diversity observed in European pigs compared with Chinese pigs17. Additionally, numerous specific alleles appear to have been fixed in European and Chinese populations after separation.Population structure and introgressionWe constructed a non-rooted phylogenetic tree based on 9.2 million population SNPs (Fig. 1a and Supplementary Fig. S6) to understand the genetic relationships and structure among Chinese pigs with different geographical distributions. The estimated phylogeny revealed that the primary division was between European and Chinese pigs, European wild boars clustered with European domestic pigs, and Chinese wild boars clustered with Chinese domestic pigs, consistent with previous studies14,17. Our results lend further support to the viewpoint that pig domestication occurred independently in western Eurasia and East Asia. Moreover, Chinese domestic breeds split on geographical grounds, namely into South and North China (CnSouth and CnNorth) subpopulations. The former encompassed all individuals from the classical South Chinese Type and some of the Central China Type. The latter comprised the remainder of Central China Type and all those from the remaining four types (North China, Lower Yangtze River Basin, Southwest, and Plateau) (Fig. 1a). The genetic relationships among Chinese indigenous pig breeds were remarkably congruent with geographic distribution. Dahua Bai (DH: Xingning City, Guangdong Province, South China) clustered with South Chinese Type breeds and Jinhua (JH: Jinhua City, Zhejiang Province, Yangtze River lower reaches) clustered with Lower Yangtze River Basin Type breeds (Fig. 1a and Table 1). Notably, DH and JH are considered to be of the Central China Type, a consideration based on coat color phenotypes4. The reference genome selected in this study was also from inbred Wuzhishan pig, which belonged to the same inbred population as WZSI used in this study. After nearly 20 generations of inbreeding, the inbred line has formed distinct genetic differentiation with other local Chinese pigs, leading to a separate cluster, including the reference genome sample and WZSI at K = 3 (Fig. 1c).Figure 1Population structure of wild and domestic pigs from different geographical regions. (a) Neighbor-joining tree of all pigs based on the 9.2 million population SNPs. The scale bar denotes p distance between individuals. (b) PCA1-2 and PCA1-3 plots of all individuals. (c) Genetic structure analysis of samples using FRAPPE, with changing ancestral populations from K = 2 to K = 5.Full size imagePrinciple component analysis (PCA) confirmed the phylogenetic analysis (Fig. 1b and Supplementary Table S6). Furthermore, a model-based clustering analysis with proportional contributions from five ancestral populations revealed the same subpopulations (CnNorth and CnSouth). Northern Chinese pigs could be further split into two subgroups (Fig. 1c): Subgroup 1 consisted of the Lower Yangtze River Basin and North China types, and Subgroup 2 comprised the Southwest and Plateau types. Features of genetic structure (Fig. 1c) and geographical distribution (Supplementary Fig. S1) confirmed the three East-Asian centers of pig domestication identified initially through mitochondrial DNA. These centers are the Mekong region18, middle and downstream regions of the Yangtze River19,20, and Tibetan highlands18,20. Thus, our study provides evidence that the classical classification scheme4,21 requires updating with genetic information.Our three analyses of population structure (phylogeny, PCA, and clustering analysis) (Fig. 1a–c) revealed that admixture likely took place in six Chinese indigenous breeds. Therefore, we employed the haplotype sharing ratio to examine putative introgression across all pairs of four populations (South China, North China, Europe, and admixed, including domestic and wild pigs) corresponding to our model-based clusters (Fig. 1c). All autosomes from South China, North China, and Europe populations contained numerous discrete introgression fragments, indicating extensive gene flow had occurred under artificial or natural evolutionary processes. Multiple large and dense regions on chromosomes 5, 14, 17, and 18 were introgressed from the European population into five Chinese breeds (Supplementary Fig. S7a–d). Similar events have been reported for Longlin22, Yuedonghei22, Min23, Kele23, and Zang/Tibetan14 breeds.We examined nucleotide variation (θπ and θw) to measure genetic diversity across three populations (wild pigs, European domestic pigs, and Chinese domestic pigs) and the two Chinese subpopulations (CnNorth and CnSouth). Tested populations were more genetically-diverse (θw/Kb: 2.01–2.80, θπ/Kb: 2.12–3.11; Supplementary Table S7) than cattle breeds Angus and Holstein24 (θw/Kb and θπ/Kb: ~1.4), dogs25 (θw/Kb: 0.61–1.28, θπ/Kb: 0.75–1.38), and giant pandas26 (θw/Kb: 1.04–1.30, θπ/Kb: 1.13–1.37). In comparison with wild and Chinese domestic pigs, European domestic pigs have a lower level of genetic diversity (θw/Kb:2.01, θπ/Kb: 2.12). We then calculated the divergence index (FST) to measure population differentiation between the different domestic pigs and wild pigs and between the two subpopulations (Supplementary Fig. S8). The highest FST (0.08) was observed between European domestic pigs and wild pigs. The LD decay rate was measured by the average distance over which the LD coefficient (r2) falls to half of its maximum value (Supplementary Fig. S9). The LD decay rate of European domestic pigs (~27.60 kb, r20.5 = 0.33) was lower than that of the other two populations (wild pigs: ~7.30 kb, r20.5 = 0.25; and Chinese domestic pigs: ~6.00 kb, r20.5 = 0.27), which might be a result of the low genetic diversity in European domestic pigs. Taken together, our results from genetic diversity and LD decay in European domestic pigs support the hypotheses of expansion from a relatively small ancestral population14,17 and a large reduction of effective population size under intensive breeding27.The bottleneck effect can greatly change the allele frequency of sites in the population, which is the main reason for the drastic change of LD in a short time28. In our study, within a short LD decayed distance (<30 Kb), wild pigs had lower r2 than Chinese pigs. However, higher r2 at a longer distance (≥30 Kb), suggests that the ancestral population from wild boars was larger than that from Chinese domestic pigs, but wild boars were subjected to narrow bottlenecks. The similar signatures of narrow bottlenecks within LD patterns have also been reported from different cattle populations24. Finally, CnNorth and CnSouth exhibited low population differentiation (FST = 0.06) and similar nucleotide diversity and LD decay rate (Supplementary Table S7 and Figs. S8 and S9b).Characterization of a large-scale LD block in the X chromosomeUsing SNP data, we identified a large-scale LD block (40.09 Mb, 44,595,487–84,684,295 bp) (Fig. 2) in the X chromosomes of all 31 pigs. This region was previously shown to have an extremely low recombination rate (48 Mb segment, 44.0–91.5 Mb)15,29, and spanned the centromeric region (47.3–49.2 Mb). We observed three major haplotypes after selecting SNP markers with inter-marker distances of 3 Kb. Haplotype S was unique to domestic and wild pigs of southern China, whereas N was present in northern Chinese wild pigs, European domestic pigs, and European wild pigs. The third was a recombinant haplotype set that included six haplotypes (N-S-1 to N-S-6) found only in northern Chinese domestic pigs (Fig. 2). These LD patterns indicate that northern Chinese domestic pigs exhibit more haplotype diversity and they corroborate previous findings of a 14 Mb X-linked sweep region12,15.Figure 2Haplotype pattern of LD block region on the chromosome X (1 SNP/0.3 Mb). Purple and blue represent the same or opposite alleles in the Wuzhishan reference genome, respectively. The percentages on the right are the proportions of samples with corresponding haplotypes in the total sample (n = 31). Red blocks represent LD blocks in the 40.09 Mb region. Haplotype S is identified in South China (domestic pigs and wild boars) (blue regions). Haplotype N is identified in European (domestic pigs and wild boars) as well as wild boar of North China (purple regions). Six derived Haplotypes (Haplotype N-S-1-6) are identified in domestic pigs of North China (purple and blue regions).Full size imageWe then used all SNP markers from the LD block to detect intervals of local breakdown in LD in the haplotype set. We identified two intervals of reduced recombination: interval 1 (left) at 46, 219, 219–46, 419, 569 bp and interval 2 (right) at 56, 819, 762–57, 752, 631 bp. The minimum distance between the two intervals was a 10.40 Mb segment (46, 419, 569–56, 819, 762 bp) (Fig. 3), a highly conserved portion of haplotype N in northern Chinese domestic pigs. Moreover, the 10.40 Mb segment is located inside the 14 Mb X-linked sweep15. Overall, we found more haplotypes (n = 8) within the 40.09 Mb LD block and a shorter conserved region (10.40 Mb) than described in the previous reports12,15,29, which were likely due to our use of high-density genetic markers from data with high sequencing depths and from obtaining a greater number of Chinese pig breeds.Figure 3Physical location ranges of recombination interval 1 (a) and interval 2 (b) (The analysis used all SNPs in the LD block region). Red and blue represent the same or opposite alleles in the Wuzhishan reference genome, respectively. (a) Three types of recombination interval 1 (Interval 1-1, Interval 1-2, Interval 1-3) are identified in the domestic pigs of North China. The maximum range of recombination interval 1 is 46,219,219-46,419,569 bp. (b) Three types of recombination interval 2 (Interval 2-1, Interval 2-2, Interval 2-3) are identified in the domestic pigs of North China. The maximum range of recombination interval 2 is 56,819,762-57,752,631 bp.Full size imageThe 40.09 Mb LD block contained 189 annotated genes, 143 (75.66%) and 108 (57.14%) of which contained SNPs and nonsynonymous substitutions, respectively. KEGG analysis mapped these 189 genes onto the Shigellosis and Neurotrophin-signaling pathway (Supplementary Tables S8 and S9). Of the 374X-chromosome QTLs in the Pig Quantitative Trait Locus database (Pig QTLdb), we aligned 247 (66.04%) to the Wuzhishan pig genome. Furthermore, 47X-chromosome QTLs overlapped with the 40.09 Mb LD block. Thirty-seven (37/47, 78.72%) and seven (7/47, 14.89%) QTLs were related to meat and carcass quality and reproduction, respectively (Supplementary Table S10). Within the meat and carcass quality associated QTLs, 26 (26/37, 70.27%) were related to fat traits (3 fat composition and 23 fatness QTLs), consistent with lipid-metabolism QTLs identified near the X-chromosome centromere30. Trait hierarchies for reproduction associated QTLs from the Pig QTLdb are divided into four categories: endocrine, litter traits, reproductive organs, and reproductive traits. In this study, the seven overlapping QTLs associated with reproduction traits were assigned to the reproductive organs, reflecting between-subpopulation (CnNorth, CnSouth, and European) differences in reproductive characters.Across CnNorth and CnSouth pigs, we identified 4,169 population-level indels in CDS regions of functional genes. After filtering out markers that covered samples less than 5 in one group to meet the minimum requirement of an expected value of chi-square statistics, 2,711 indels remained. Six differed significantly between the two subpopulations, and five of these were distributed in three gene loci (ENSSSCG00000012830, HUWE1, and ITIH5L) in the 10.40 Mb conserved region (Supplementary Table S11). The first locus contained three indels that were matched against the InterPro database to reveal two specific cold-shock protein domains (IPR002059 and IPR011129). Variants of these genes in the CnNorth pigs were also found in northern Chinese wild pigs and European domestic and wild pigs.We next selected the top 100 SVs out of 64,876 population-level SVs that exhibited significantly non-random distribution (χ2 test with FDR correction, P < 0.01). Thirty-four of these SVs were located in the X chromosome (Supplementary Table S12), with 32 in the 10.40 Mb conserved region. The conserved region contained 63 annotated genes, and four (EDA, HEPH, ARHGEF9, and HUWE1) overlapped with six SVs that exhibited very high between-group differences (P = 8.53 × 10-4) (Supplementary Table S13). We identified two large loss-of-function deletion patterns (382 bp: 56,650,381–56,649,999, and 487 bp: 56,621,617–56,621,130, Supplementary Table S13) on EDA and found that they were fixed only in CnNorth pigs. The EDA signaling pathway is involved in ectodermal-organ (hair, teeth, and exocrine glands) development31,32, and EDA defects result in Tooth Agenesis32. Our findings are consistent with archaeological evidence of different tooth structural characters between CnNorth and CnSouth pigs4.Identification of candidate genes for body sizeOur sample was split into small pigs (adult body length ≤100 cm, height ≤50 cm; N = 7) and large pigs (adult body length ≥120 cm, height ≥65 cm; N = 7), based on early phenotype characterization records21 and our own measurements (Supplementary Table S14). We then identified 115 nonsynonymous substitutions, distributed in 95 gene regions, that differed in allele frequency between large versus small pigs (>80% in one group, approaching fixation; <20% in the other) (Supplementary Table S15). These nonsynonymous substitutions were putative candidate polymorphisms that resulted in size differences. Indeed, two genes (LEPR and FANCC) overlapping with nonsynonymous substitutions are reported as associated with body growth and development in some mammals33,34. In humans, impaired LEPR function exerts a strong negative effect on ponderal index at birth and height in adolescence34. Likewise, FANCC plays a major role in skeletal formation, and thus affects human height35,36.We then analyzed differences (χ2-test with Bonferroni’s correction) in frequency of indels and SVs between large and small pigs, to understand their effects on body size. We found significant (P < 0.05) between-size-group differences for 10 indels and 20 SVs, located within 7 and 10 functional genes, respectively (Supplementary Tables S16 and S17). For all the seven small pigs, we identified a 4 bp insertion in the third exon of COL1A1. COL1A1 is an α1(I) protein chain of type I collagen and a major structural component of bone. Nonfunctional COL1A1 markedly reduces skeletal mineral density and body height37,38. We also found a 430 bp deletion in the third intron of the gene encoding propionyl CoA caboxylase α subunit (PCCA). A genetic defect in PCCA causes propionic acidemia, a condition that can lead to bone disease and growth failure39.Materials and MethodsSamplesAll animals used in this study were reared and euthanized with the approval of the College of Animal Science, South China Agricultural University. All experiments were performed in accordance with ‘The Instructive Notions with Respect to Caring for Laboratory Animals’, issued by the Ministry of Science and Technology of the People’s Republic of China. To clarify the genetic structure of Chinese pigs across different geographical locations, we selected individuals that represent all six Chinese indigenous types4: South Chinese (n = 10), North China (n = 2), Lower Yangtze River Basin (n = 2), Central China (n = 3), Southwest (n = 1), Plateau (n = 2). The proportion of representative breeds represented in our study from each type was shown in Supplementary Table S1. We also included samples from southern and northern Chinese wild pigs (n = 4), as well as European wild and commercial pigs (n = 7) (Table 1 and Supplementary Fig. S1). Altogether, data from 31 individual animals were used in this study: (i) 24 sampled from 22 breeds, which were handled by the South China Agricultural University, Guangzhou, People’s Republic of China (Table 1 and Supplementary Fig. S1) and (ii) seven (one pig per breed) downloaded from the Wageningen University Porcine Re-sequencing Phase 1 Project (http://www.ebi.ac.uk/ena/data/view/ERP001813)12,17 with the highest sequencing depths to supplement the breeds sampled here (Table 1). Seven small pigs and seven large pigs were used to detect candidate genes for body size (Supplementary Table S14). Body size data were obtained for 14 pigs, 11 from the book Animal genetic resources in China: pigs21, and three were measured according to the technical specifications for the registration of breeding pigs (NY/T 820-2004, 2004). A completed ARRIVE guidelines checklist is included in Table 1.DNA isolation and genome sequencingGenomic DNA was extracted from ear tissue of live collection using a phenol-chloroform-based method. For each sample, 1–15 µg of DNA was sheared into 200–800 bp fragments using the Covaris system (Life Technologies). Fragments were then treated according to the Illumina DNA-sample-preparation protocol. For library construction, fragments were end-repaired, A-tailed, ligated to paired-end adaptors, and PCR-amplified with 500 bp inserts. Sequencing was performed to generate 100 bp paired-end reads on the HiSeq 2000 platform (Illumina), following the manufacturer’s protocol.Sequence alignment and genotype callingFiltered reads were aligned to the Wuzhishan pig draft genome assembly (minipig_v1.0)40 using the Burrows-Wheeler Aligner41. This genome was selected as the reference7,40 after considering the geographical distance and genetic divergence among the 31 breeds (Table 1 and Supplementary Fig. S1 and Table S1).Aligned bam files were sorted and indexed in Picard-tools version 1.117. Two GATK (Genome Analysis Toolkit version 2.4–942 modules, RealignerTargetCreator and IndelRealigner), were used to realign the SNPs around indels in bam results. To obtain high-quality variants, additional GATK modules HaplotypeCaller and SAMtools43 were used to call variants for each sample. Only concordance variants were selected, and SNPs were filtered with the parameter “QD < 2.0 | | FS > 30.0 | | MQ < 40.0 | | DP < 6 | | DP > XXX | | ReadPosRankSum < -8.0 | | BaseQRankSum < -8,” while indels were filtered with “QD < 2.0 | | FS > 30.0 | | ReadPosRankSum < -8.0.” These variants were used to perform base quality score recalibration (BQSR), and resultant reads were applied calling population variants, done with the GATK HaplotypeCaller module using the parameter “–genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30.”To detect structural variants, we followed an existing method44, with some modifications. Reads were assembled into contigs and scaffolds using default parameters in SOAPdenovo. The assembled scaffold was mapped to the reference genome in BLAT45, with the –fastmap option.Criteria for determining the most well-aligned scaffold included coverage length in a given region and high contig support. Selected scaffolds and reference-genome regions with the highest alignment were extracted and aligned to each other in LASTZ (http://www.bx.psu.edu/miller_lab/). Unmapped scaffolds were further aligned against the reference genome using BLASTn. Structural variants were extracted based on all aligned regions.Phylogenetic and population genetic analysesGenetic structure was inferred from high-density SNP data in FRAPPE46, a program that applies maximum likelihood and expectation-maximization to estimate individual ancestry and admixture proportions. To explore individual convergence, we predefined the number of genetic clusters from K = 2 to K = 5. The maximum iteration of the expectation-maximization algorithm was set to 10,000.A phylogenetic tree was generated from population-level SNPs in TreeBeST (http://treesoft.sourceforge.net/treebest.shtml), under the p-distances model. Population-level SNPs were then subjected to PCA in EIGENSOFT47, and eigenvectors were obtained using the R (https://www.r-project.org/) function eigen.To evaluate LD decay, Haploview48 was used to calculate the squared correlation (r2) between any two loci. Average r2 was calculated for pairwise markers in a 5 Kb window and averaged across the whole genome. LD blocks were defined by the confidence interval method of Gabriel et al.49 and implemented in the Haploview 4.2 software (https://www.broadinstitute.org/haploview/haploview). Haplotype phase are inferred using a standard EM algorithm from the Haploview 4.2 software. The software script is as follows: “ava -jar Haploview.4.2.jar -n -pedfile X_112.ped -info X_112.info -maxdistance 500 -minMAF 0.0 -hwcutoff 0.001 -log X_112.log -blockoutput GAB -memory 19240 -pairwiseTagging -hwcutoff 0.00000”.Gene and QTL annotationPathway analyses of candidate genes were performed using KEGG (https://www.genome.jp/kegg/pathway.html). KEGG analysis is mainly performed by the following three steps: 1) Extract the nucleoside and protein sequences of the target gene, 2) Align the protein sequences to the KEGG animal database with the alignment software BLAST3, 3) Classify each gene according to the annotation information. Additionally, identified QTLs were functionally characterized using Pig QTLdb (https://www.animalgenome.org/cgibin/QTLdb/SS/index, Release 23, Apr 21, 2014), specifically with coordinate conversion of the Wuzhishan genome to the European-Duroc reference genome (Sscrofa10.2). Indels were matched to the InterPro database using EBI InterProScan (https://www.ebi.ac.uk/interpro/search/sequence-search).Introgression analysisMethods described in a published study50 were used. We applied a likelihood ratio test to study the ancestral contribution of groups to the genome of each individual pig. All putative introgressions between group pairs (North China, South China, and Europe) were examined. For every 100 Kb window containing at least 10 SNPs and when at least three comparisons were possible per group, we calculated the ratio of the average sharing per pig with its own and another group. Regions with an average sharing ratio of <0.8 were defined as introgressions. Shared introgression frequency was plotted and tabulated. Introgression length and number per pig were also tabulated. Regions of extensive haplotype sharing (≥90% shared SNPs) were considered introgressed regions for each group pair.

Data availability

The datasets generated and analysed during the current study are available from the corresponding author on reasonable request.

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Download referencesAcknowledgementsThis work was supported by the Key Foundation for Basic and Application Research in Higher Education of Guangdong, China (2017KZDXM009); the Team Project of Guangdong Agricultural Department, China (2017LM2148); the Provincial Agricultural Science Innovation and Promotion Project in 2018 (2018LM2150); the Guangdong Provincial Key Area Research and Development Program (2018B020203002); and the South China Agricultural University Major Project for International Science and Technology Cooperation Cultivation (2019SCAUGH01). The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript.Author informationAuthor notesThese authors contributed equally: Xiong Tong and Lianjie Hou.Authors and AffiliationsNational Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, 510642, ChinaXiong Tong, Lianjie Hou, Bo Huang & Chong WangState Key Laboratory of Agricultural Genomics, BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, ChinaWeiming He & Chi ZhangState Key Laboratory of Livestock and Poultry Breeding, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, ChinaXiong TongCollege of Animal Science and Technology, Northwest A&F University, Yangling, 712100, ChinaChugang MeiDepartment of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, 1955 East-West Road, AgSci. 415J, Honolulu, HI, 96822, USAChingyuan HuAuthorsXiong TongView author publicationsYou can also search for this author in

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PubMed Google ScholarContributionsC.W. and X.T. conceived and designed the experiments. W.H. and C.Z. performed variation identification and population analyses. W.H., X.T., C.Z. and B.H. contributed to computational analyses. X.T. and L.H. collected samples and prepared them for sequencing. C.W., C.M. and C.H. provided suggestions and reviewed the manuscript. X.T. wrote the manuscript, and C.M. help revised the manuscript. All authors read and approved the final manuscript.Corresponding authorCorrespondence to

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Reprints and permissionsAbout this articleCite this articleTong, X., Hou, L., He, W. et al. Whole genome sequence analysis reveals genetic structure and X-chromosome haplotype structure in indigenous Chinese pigs.

Sci Rep 10, 9433 (2020). https://doi.org/10.1038/s41598-020-66061-2Download citationReceived: 02 September 2019Accepted: 14 May 2020Published: 10 June 2020DOI: https://doi.org/10.1038/s41598-020-66061-2Share this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard

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