尼日利亚家养动物母系遗传多样性及进化研究：以狗和珍珠鸡为例
文献类型：学位论文
| 作者 | ADENIYI CHARLES ADEOLA |
| 学位类别 | 博士 |
| 答辩日期 | 2015-05 |
| 授予单位 | 中国科学院研究生院 |
| 授予地点 | 北京 |
| 导师 | 张亚平 |
| 关键词 | 线粒体DNA 单倍群 系统发育树 尼日利亚 家犬 珍珠鸡 |
| 其他题名 | Matrilineal diversity and evolution of domesticated animals in Nigeria with a focus on dogs and helmeted guinea fowl |
| 中文摘要 | 在非洲大陆分布有众多家养动物，其中包括家犬，家猪，家牛，家鸡，家猫，珍珠鸡等。目前，非洲家养动物的起源和群体历史演变的问题仍待解决。线粒体DNA（mtDNA）是一个用来揭示母系遗传变异的分子标记，从而可用于追溯群体历史。因此，我们将通过分析mtDNA分子标记来探讨西非尼日利亚的家犬和珍珠鸡的生物多样性，基因流和群体结构。 第一章概述了尼日利亚的地理背景、研究家养动物的意义以及mtDNA分子。在第二章，我们回顾了家养动物的驯化过程以及相关的考古学和遗传学的研究方法。我们还对非洲家养动物的驯化历史以及适应性演化（如抗蜱、抗病性等）进行了介绍。 第三章，为了探讨非洲家犬（Canis lupus familiaris）祖先的起源和群体历史，我们分析了345条尼日利亚家犬和已发表的来自非洲其他地区、欧洲和西亚地区的家犬线粒体控制区序列。结果显示，尼日利亚家犬都可以被划分至A、B、C、D4个单倍群（haplogroup）中。非洲家犬中没有检测到来自非洲狼（Canis lupus lupaster）的母系遗传贡献。单倍群D线粒体基因组分析表明北欧和西非的家犬之间存在目前关系。结合人类分子学证据，我们推测单倍群D1中的非洲家犬可能是在后冰川时期伴随着欧洲西南部狩猎者进行扩散。 珍珠鸡是非洲起源的家禽。作为重要的养殖对象，非洲珍珠鸡的研究还有待开展。在第四章中，我们探讨了家养珍珠鸡（Numida meleagris）母系遗传多样性，系统发育及种群结构。本研究分析了尼日利亚珍珠鸡7个不同种群的215条线粒体控制区序列，并与4条肯尼亚和22条中国的珍珠鸡线粒体控制区序列进行了比较。我们一共发现了22个单倍型；大部分的mtDNA世系可以被划分到两个单倍群A和B。尼日利亚珍珠鸡的单倍型多样度和核苷酸多样度分别是0.693和0.160，其较低的遗传多样性可能是由于近期驯化和家禽的快速扩散导致的。 第五章，我们通过长片段PCR结合高通量测序的方法测定了珍珠鸡的线粒体基因组。所测定的珍珠鸡线粒体基因组（16722bp）由13个蛋白质基因，22个tRNA基因，2个rRNA基因和控制区序列组成，其控制序列与典型的脊椎动物排序一致。这种方法能够快速获得珍珠鸡线粒体基因组序列，有望能促进了其系统发育，种群遗传和保护的相关研究。 |
| 英文摘要 | There are many domestic animals that have lived with human on the African continent. These include dog, pig, cattle, chicken, cat, guinea fowl and so on. In recent time, origin and subsequent demographic history of African domesticated animals still remain unsolved. Mitochondrial DNA (mtDNA) marker is a very powerful molecular tool that can reveal huge amounts of matrilines genetic variability within and among conspecific populations. Therefore, I use this tool to access the biodiversity, genogeography, and population structures of two domestic animals in African: village dogs (Canis lupus familiaris) and domesticated helmeted guinea fowl (Numida meleagris) from Nigeria, West Africa. Chapter 1 is an overview of the geography of Nigeria, purpose of studying domestic animals, mtDNA as a molecular marker. In chapter 2, I review animal domestication as a co-evolutionary process and mention adaptive characters such as resistance to tick and some mortal infectious diseases, dwarfing and increase in fecundity that domestic animals in African have evolved. I highlight some of the various transformations that follow domestication process and describe how archaeological and genetic markers have detected domestication in animals. I also explain molecular markers for genetic diversity studies. Thereafter, I briefly discuss genome evolution through admixture and introgression. I conclude with discussions on domestication history of animal species in Africa. In chapter 3, I take a comprehensive look into village dogs from Nigeria, West Africa plus village dogs from other parts of Africa, Europe and West Asia. I aim to trace the source (s) of ancient genetic component in African dogs in order to have an insight into their origin. Herein, I analyze variation in mtDNA D-loop sequences from 345 Nigerian village dogs plus 1106 published sequences from other parts of Africa, Europe and West Asia. All Nigerian dogs assign into one of four major haplogroups (matrilines haplogroups): A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African wolf (Canis lupus lupaster). The analyses of near-complete mitochondrial genomes of haplogroup D reveal that North European and West African dogs coalesce into sub-haplogroup D1 around 12,000 years ago. Incorporating molecular anthropological evidence, we propose that haplogroup D1 in West African dogs could be traced back to the late-glacial dispersals, potentially accompanied with hunter-gatherers, from southwestern Europe. Chapter 4 focuses on the domesticated N. meleagris populations from Nigeria, Kenya and China to explore the matrilineal genetic diversity, phylogeny and population structure. I study N. meleagris because despite the vital role it plays in the poultry industry, little is known about its genome and particularly N. meleagris from West Africa one of the proposed region of its domestication. Herein, I analyze genetic diversity of 215 mtDNA D-loop sequences from seven different populations of N. Meleagris in Nigeria and compare with results of samples collected in Kenya (n=4) and China (n=22). The total of 241 sequences assign into 22 distinct haplotypes. Haplotype and nucleotide diversity in Nigeria are 0.693 and 0.160, respectively. The network group most matrilines into two main haplogroups A and B. There was absence of geographic signal and two haplotypes dominated across all locations with the exception of Kebbi population in the North-West of the country and AMOVA also confirm this observation (FST=0.035). The low genetic diversity with lack of maternal genetic structure may be as a result of recent domestication and rapid dispersal of free-range poultry. The differentiation of Kebbi population may probably be due to low frequency of one of the dominant haplotype and presence of unique haplotypes. Chapter 5 explores the mitochondrial genome of N. meleagris from Nigeria. I aim to sequence the complete mitochondrial genome of N. meleagris using a long-PCR based next generation sequencing technique. I hope this approach will enable rapid collection of mitochondrial genome sequences to facilitate studies on phylogenetic relationships, genetic diversity, and conservation of N. meleagris. I determine the complete mtDNA sequence (16,722 bp) of the N. meleagris. It has 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region which was typical vertebrate arrangement. The protocol and procedure to achieve this mitochondrial genome are provided. |
| 源URL | [http://159.226.149.26:8080/handle/152453/10187]  |
| 专题 | 昆明动物研究所_分子进化基因组学 |
| 推荐引用方式 GB/T 7714 | ADENIYI CHARLES ADEOLA. 尼日利亚家养动物母系遗传多样性及进化研究：以狗和珍珠鸡为例[D]. 北京. 中国科学院研究生院. 2015. |
入库方式： OAI收割
来源：昆明动物研究所
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。