家马的起源历史与品种驯化特征

在家犬(Canis lupus familiaris)、牛(Bos taurus)、猪(Sus scrofa domesticus)、绵羊(Ovis aries)、山羊(Capra hircus)等家养动物之后,家马(Equus caballus)才被人类成功驯化。虽然驯化历史很短,但其对人类社会文明发展变革的影响却最大。家马出色的负重移动能力使人类社会由固定的农耕模式向移动分享模式过渡,使历史发展进入了快车道,因此其起源驯化历史一直备受关注。然而由于家马直系同源野生种早已灭绝,加之现代品种化培育引起遗传多样性骤减,使得相关研究长期争议不断。随着测序技术的不断发展和古代样品的逐步丰富,目前对家马起源驯化过程、群体遗传结构等方面的研究越来越深入。本文从核基因、mtDNA、Y染色体、古DNA等不同层面综述了家马起源与驯化历史方面的研究进展,从品种分化状况、群体演化特征等方面讨论了现代家马品种的群体遗传结构,最后总结了马匹毛色、速度、体型等重要表型性状的遗传基础,以期为今后家马的起源驯化研究、种质资源保护与开发、品种优化方向、现代马业发展等方面提供参考。     

家养动物驯化起源的研究方法与进展

驯化动物伴随了人类上万年的进化历程。在驯化过程中, 家养动物表型和行为特征发生巨大改变, 并与人类生产生活的进步相适应。研究动物驯化问题对于了解遗传多样性及适应性进化, 解析复杂性状的遗传机制等具有重要的意义, 成为生物学领域的重点研究内容之一。本文专注于动物驯化的初始阶段, 首先介绍了驯化起源的时间与地点、驯化途径和驱动因、驯化后的扩散和品种选育; 其次从驯化对象的角度着重介绍了考古学、分子和群体遗传学两方面的家养动物驯化起源的研究策略、优势与不足, 以及未来的发展方向; 最后, 我们综合多方面的证据, 介绍了在中国驯化的家猪(Sus domesticus)和家鸡(Gallus gallus domesticus)以及其他主要家养动物考古和分子水平上驯化起源的研究进展。本文整合多种证据为家养动物驯化起源的研究提供了相对完整的视角和新的思路。     

家养动物的起源与驯化研究进展

动物的驯化是新石器时代农业革命的主要内容之一, 导致了人类生活方式从狩猎向畜牧的转变。开展家养动物起源与驯化的研究, 不仅有助于了解人类社会的发展史和人工选择下动物的进化过程, 而且有助于开展家养动物的良种选育和遗传多样性保护, 因此该研究领域受到了人们的长期关注。近年来, 随着更多考古证据的发现与分子遗传学的发展, 人们对于家养动物的起源与驯化有了更深入的认识。本文对家养动物起源与驯化研究中一些基本问题的研究方法和进展进行了综述。文章第一部分介绍了家养动物的野生祖先、起源地、起源时间、建群者大小和扩散路线等问题; 第二部分则涉及家养动物驯化的条件、过程、性状改变及其遗传机制等方面。最后指出了家养动物起源与驯化研究中依然存在的问题, 并对未来研究发展的趋势进行了讨论。     

作物驯化的遗传学研究及其在大豆育种中的应用

驯化遗传学是进化生物学研究的一个重要分支, 对作物驯化历程进行深入探索, 可以更好地认识人类早期农耕文明的产生和发展, 了解物种的形成乃至生命的起源和进化, 对指导人们利用野生资源来改良现有的栽培作物和培育新的有价值的品种也具有重要的意义。本文综述了作物驯化的遗传学研究内容和进展, 以及重要作物大豆驯化起源的研究概况, 探讨了目前作物驯化研究对大豆驯化遗传学及野生大豆资源综合利用的指导意义。     

作物驯化的遗传学研究及其在大豆育种中的应用

驯化遗传学是进化生物学研究的一个重要分支,对作物驯化历程进行深入探索,可以更好地认识人类早期农耕文明的产生和发展,了解物种的形成乃至生命的起源和进化,对指导人们利用野生资源来改良现有的栽培作物和培育新的有价值的品种也具有重要的意义。本文综述了作物驯化的遗传学研究内容和进展,以及重要作物大豆驯化起源的研究概况,探讨了目前作物驯化研究对大豆驯化遗传学及野生大豆资源综合利用的指导意义。     

基于基因组SNPs对东亚家马不同群体遗传多样性的评估

家马地方品种的遗传多样性是动态演变的, 并与其育种模式息息相关; 在过去约300年中, 育种者培育了具突出表型特征的标准化培育品种, 该类型品种对家马地方品种的繁育产生了巨大影响, 这是导致家马地方品种遗传多样性下降及遗传分化的主要因素之一。本研究采集了5个东亚家马地方品种(蒙古马、哈萨克马、河曲马、藏马和西南马)、2个西亚家马品种(阿拉伯马和阿哈尔捷金马)以及2个欧洲家马品种(设特兰矮马和克莱斯黛尔马)的70个样品, 并整合之前所发表的100匹内蒙古地区家马不同群体单核苷酸多态性(SNPs)数据集, 通过全基因组重测序和生物信息学方法分析了东亚家马不同群体的遗传多样性。研究发现东亚家马地方品种具有较丰富的遗传多样性, 相比欧洲和西亚品种产生了显著的遗传分化, 其中蒙古高原群体的遗传多样性最为丰富; 受杂交改良影响, 内蒙古不同群体间产生了一定程度的遗传分化; 河曲马和藏马的遗传背景最为单一, 受引种杂交繁育影响较小。本研究评估了东亚家马地方品种的遗传多样性分布格局和演化特征, 可为建立家马地方种质核心保护群体以及培育新品种提供遗传学理论支持。     

中国濒危兽类保护遗传学研究进展与展望

我国是全球生物多样性大国,拥有包括大熊猫、金丝猴、华南虎、麋鹿、白鱀豚等特有物种和旗舰物种在内的丰富兽类资源。近几十年来,土地利用模式转变、盗猎、环境污染、气候变化等因素使许多兽类物种面临生存威胁,导致物种遗传多样性丧失。而遗传多样性是生物多样性的基本组成部分,决定了物种和种群能否长期生存。保护遗传学作为保护生物学的一大分支学科,旨在通过遗传学分析探明种群遗传变异和物种濒危的遗传学机制。近40年来,随着研究手段和技术的不断发展,我国兽类保护遗传学在遗传多样性和近交水平评估、景观遗传学、生态遗传学和圈养种群遗传管理等方面都取得了重要成果。然而,未来人类社会发展可能为濒危兽类带来的威胁依然存在,高通量测序等新技术的进一步发展则能够帮助我们更加深入地了解濒危物种和种群遗传适应与濒危机制,从而实现对濒危兽类的有效管理与保护。     

水稻驯化与长江文明

水稻(即亚洲栽培稻Oryza sativa)是世界上最重要的粮食作物之一, 全球有超过半数以上人口以稻米为食。关于水稻是何时、何地、在什么环境下开始驯化等问题一直是学术界关注的热点。得益于分析技术的进步, 近年来考古学和遗传学研究在水稻驯化起源问题上取得了重要进展。本文简要综述了有关长江流域的水稻驯化起源的遗传学和考古学的研究进展, 并讨论了水稻驯化与稻作文化及长江文明的关系。遗传学研究结果认为水稻(粳稻)最早起源于中国长江流域及以南地区(珠江流域), 考古学证据则表明水稻最先于10,000-8,000 BP在中国长江流域被驯化, 水稻驯化和稻作农业的发展催生了长江文明。这些进展促进了我们对水稻驯化、稻作文化和长江文明的认识, 对长江流域重要植物资源的保护也有启示意义。     

马的演化与遗传多样性研究

马在人类社会早期的经济和军事方面发挥过重要的作用。同时,马的形态进化一直是进化论的最早例证。然而,随着马在现代社会中实用性的减少和重要性的下降,马种资源正在严重流失。笔者回顾了马属和家马在古生物、考古、遗传与进化等方面的研究情况,以期为马种资源保护提供参考。     

遗传伦理问题起源的研究与对策

遗传伦理问题是生命科学领域最具争议并最难以妥善解决的问题之一。近年来, 此类问题的研究主要是围绕遗传伦理问题的种类及解决方法进行的。但关于遗传伦理问题起源的系统研究尚不多见, 这也使相应对策的提出显得缺乏理论支撑。文章从人类生物进化与文化进化的双重角度深入探讨了遗传伦理问题发生的进化根源和演化规律。人类是生物进化与文化进化的双重产物, 是地球上唯一既具有生物属性又具有文化属性的物种。通过对人类生物进化与文化进化及其生物属性与文化属性特点的比较研究, 文章提出了任何伦理问题都可以从人类的生物进化与文化进化之间相互作用所产生的冲突中找到其发生根源的观点, 其目的是为研究遗传伦理问题及其对策的提出寻求理论和实践上的依据。同时, 提出了一系列关于遗传伦理问题的对应策略。文章的最终目的并非仅仅为某种观点能被接受, 而是希望通过对遗传伦理问题及其起源的了解和认识, 使遗传学领域的决策者和研究者更具使命感与责任感, 使一般公众对遗传学研究及其应用少一些误解, 多一些理性, 从而使遗传学事业能健康、持续发展, 造福人类。     

Multiple maternal origins of native modern and ancient horse populations in China

To obtain more knowledge of the origin and genetic diversity of domestic horses in China, this study provides a comprehensive analysis of mitochondrial DNA (mtDNA) D-loop sequence diversity from nine horse breeds in China in conjunction with ancient DNA data and evidence from archaeological and historical records. A 247-bp mitochondrial D-loop sequence from 182 modern samples revealed a total of 70 haplotypes with a high level of genetic diversity. Seven major mtDNA haplogroups (A–G) and 16 clusters were identified for the 182 Chinese modern horses. In the present study, nine 247-bp mitochondrial D-loop sequences of ancient remains of Bronze Age horse from the Chifeng region of Inner Mongolia in China ( c. 4000–2000a bp ) were used to explore the origin and diversity of Chinese modern horses and the phylogenetic relationship between ancient and modern horses. The nine ancient horses carried seven haplotypes with rich genetic diversity, which were clustered together with modern individuals among haplogroups A, E and F. Modern domestic horse and ancient horse data support the multiple origins of domestic horses in China. This study supports the argument that multiple successful events of horse domestication, including separate introductions of wild mares into the domestic herds, may have occurred in antiquity, and that China cannot be excluded from these events. Indeed, the association of Far Eastern mtDNA types to haplogroup F was highly significant using Fisher's exact test of independence ( P  = 0.00002), lending support for Chinese domestication of this haplogroup. High diversity and all seven mtDNA haplogroups (A–G) with 16 clusters also suggest that further work is necessary to shed more light on horse domestication in China.     

European domestic horses originated in two holocene refugia

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.     

A microsatellite analysis of five Colonial Spanish horse populations of the southeastern United States

The domestic horse (Equus caballus) was re-introduced to the Americas by Spanish explorers. Although horses from other parts of Europe were subsequently introduced, some New World populations maintain characteristics ascribed to their Spanish heritage. The southeastern United States has a history of Spanish invasion and settlement, and this influence on local feral horse populations includes two feral-recaptured breeds: the Florida Cracker and the Marsh Tacky, both of which are classified as Colonial Spanish horses. The feral Banker horses found on islands off the coast of North Carolina, which include, among others, the Shackleford Banks, the Corolla and the Ocracoke, are also Colonial Spanish horses. Herein we analyse 15 microsatellite loci from 532 feral and 2583 domestic horses in order to compare the genetic variation of these five Colonial Spanish Horse populations to 40 modern horse breeds. We find that the Corolla horse has very low heterozygosity and that both the Corolla and Ocracoke populations have a low mean number of alleles. We also find that the Florida Cracker population has a heterozygosity deficit. In addition, we find evidence of similarity of the Shackleford Banks, Marsh Tacky and Florida Cracker populations to New World Iberian horse breeds, while the origins of the other two populations are less clear.     

High microsatellite and mitochondrial diversity in Anatolian native horse breeds shows Anatolia as a genetic conduit between Europe and Asia

The horse has been a food source, but more importantly, it has been a means for transport. Its domestication was one of the crucial steps in the history of human civilization. Despite the archaeological and molecular studies carried out on the history of horse domestication, which would contribute to conservation of the breeds, the details of the domestication of horses still remain to be resolved. We employed 21 microsatellite loci and mitochondrial control region partial sequences to analyse genetic variability within and among four Anatolian native horse breeds, Ayvac?k Pony, Malakan Horse, H?n?s Horse and Canik Horse, as well as samples from indigenous horses of unknown breed ancestry. The aims of the study were twofold: first, to produce data from the prehistorically and historically important land bridge, Anatolia, in order to assess its role in horse domestication and second, to analyse the data from a conservation perspective to help the ministry improve conservation and management strategies regarding native horse breeds. Even though the microsatellite data revealed a high allelic diversity, 98% of the genetic variation partitioned within groups. Genetic structure did not correlate with a breed or geographic origin. High diversity was also detected in mtDNA control region sequence analysis. Frequencies of two haplogroups (HC and HF) revealed a cline between Asia and Europe, suggesting Anatolia as a probable connection route between the two continents. This first detailed genetic study on Anatolian horse breeds revealed high diversity among horse mtDNA haplogroups in Anatolia and suggested Anatolia’s role as a conduit between the two continents. The study also provides an important basis for conservation practices in Turkey.     

Asian horses deepen the MSY phylogeny

Humans have shaped the population history of the horse ever since domestication about 5500 years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y‐chromosomal phylogeny of modern horses based on 1.46 Mb of the male‐specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 ± 872 years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.     

Autosomal genetic diversity in non‐breed horses from eastern Eurasia provides insights into historical population movements

Many events in the history of eastern Eurasia, including the process of domestication itself, the initial spread of domestic horses and subsequent movements, are believed to have affected the genetic structure of domestic horse populations in this area. We investigated levels of within‐ and between‐population genetic diversity in ‘non‐breed horses’ (working horses sampled in remote areas) from 17 locations in Asia and parts of Eastern Europe, using 26 autosomal microsatellite loci. Non‐breed horses have not been subject to the same intensity of artificial selection and closed breeding as have most breed animals and are thus expected to better reflect the population history of domestic horses. Despite geographic distances of between 300 and 7000 km between sampling locations, pairwise F _ST was very low (range: <0.001 to ?0.033), suggesting historically high levels of gene flow. Our analyses of non‐breed horses revealed a pattern of isolation by distance and a significant decline in genetic diversity (expected heterozygosity and allelic richness) from east to west, consistent with a westward expansion of horses out of East Asia. Although the timing of this putative expansion is unclear, our results highlight the benefit of studying animals that do not belong to particular breeds when investigating aspects of a population's history.     

Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics

The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n?=?6) and additional Mongolian (n?=?2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200–63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000–10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.     

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.     

Characterization of cytochrome b diversity in Chinese domestic horses

Previous mitochondrial DNA (mtDNA) D‐loop and microsatellite studies have shown that Chinese horses have multiple maternal origins and high genetic diversity. To better characterize maternal genetic origins and diversity of Chinese domestic horses, we conducted a comprehensive analysis of 407 complete 1140 bp sequences of the horse mitochondrially encoded cytochrome b (CYTB) gene, including 323 horses from 13 Chinese indigenous breeds and 84 reference sequences from GenBank. A total of 114 haplotypes were identified, of which 73 appeared among the 13 Chinese horse breeds. The high mitochondrially encoded cytochrome b haplotypic diversity suggests multiple maternal origins in Chinese horses.     

Ancient Genomes Reveal Unexpected Horse Domestication and Management Dynamics

The horse was essential to past human societies but became a recreational animal during the twentieth century as the world became increasingly mechanized. As the author reviews here, recent studies of ancient genomes have revisited the understanding of horse domestication, from the very early stages to the most modern developments. They have uncovered several extinct lineages roaming the far ends of Eurasia some 4000 years ago. They have shown that the domestic horse has been significantly reshaped during the last millennium and experienced a sharp decline in genetic diversity within the last two centuries. At a time when no truly wild horses exist any longer, this calls for enhanced conservation in all endangered populations. These include the Przewalski's horse native to Mongolia, and the many local breeds side-lined by the modern agenda, but yet representing the living heritage of over five millennia of horse breeding.