Knowledge Resource Center for Ecological Environment in Arid Area
| 三趾跳鼠（Dipus，Dipodinae，Dipodidae）系统发育、 分类重估和谱系地理学研究 | |
| 其他题名 | Phylogeny，taxonomic reassessment and phylogeography of jerboa（Dipus，Dipodinae，Dipodidae） |
| 程继龙 | |
| 出版年 | 2018 |
| 学位类型 | 博士 |
| 导师 | 杨奇森 |
| 学位授予单位 | 中国科学院大学 |
| 中文摘要 | 物种是进化生物学研究的基本单元与核心。整合分类与谱系地理学的结合，能够在研究物种进化历史与分布格局的基础上，对传统分类系统进行重新梳理和样品鉴定以及揭示隐存种的存在。近年来对北美、澳洲、北非等荒漠地区的生物多样性和谱系地理的研究发现，荒漠地区并非“荒芜之地”，荒漠物种通常也有着独特的进化历史和分布格局。亚洲内陆干旱区深居欧亚大陆腹地，区域内高山巨盆相间、沙漠间断分布、高原波状起伏、草原荒漠渐变。与北半球同纬度的欧洲和北美地区相比，新近纪以来复杂的地质历史和更新世气候旋回对亚洲内陆干旱区的塑造明显不同，因而该地区生物的历史地理分布和进化历程也呈现出显著的区域特征。三趾跳鼠属（Dipus）广泛分布于亚洲内陆干旱区，是古北区分布范围最大的荒漠啮齿动物，也是研究亚洲内陆干旱区地质历史对该地区物种现代分布格局形成的理想材料。但是，随着对三趾跳鼠研究的增多，国内外学者发现了很多分类上的问题。因此，本研究的目的是以三趾跳鼠属为研究对象，从时间尺度和空间尺度上，系统探究亚洲内陆干旱区的地质历史和气候变化过程如何塑造该地区物种分化格局和现代分布格局，寻找该区域物种进化历史的普遍规律。同时利用整合分类和谱系地理学的方法，厘清这一类群的分类问题，为荒漠地区生物多样性的研究提供新的例证。本研究首先对三趾跳鼠属的系统发育关系进行构建并重估属内分类问题。通过对其各大分布区、不同亚种的模式产地的采样以及从GenBank上获取的国外分布区样品的序列，本研究共收集了383号样品的2个线粒体基因（共1774bp）和6个核基因片段（共5561bp）。同时，我们还收集了保存于中国科学院动物研究所国家动物博物馆兽类标本馆、莫斯科国立大学动物博物馆、俄罗斯科学院动物研究所（圣彼得堡）和英国自然历史博物馆的174个个体的体型指标、152个个体的头骨形态指标以及191个个体的头骨图像照片等形态信息。本研究使用“候选种”的方法，以高度分化的mtDNA和过去研究中鉴定的亚种为起点，基于贝叶斯法和最大似然法重建三趾跳鼠的系统发育关系，用五种不同的物种发现分析和两种物种验证分析重建物种树进行物种界定。三趾跳鼠属长期以来一直被认为是一单型属，但本研究发现，三趾跳鼠属内表现出较高的遗传分化水平，线粒体基因树聚成四个支持率极高的单系群，其相互间的遗传距离可达10%以上，而物种界定则认为其中存在5-11个物种。以这四个单系群为基础，我们用传统形态统计和几何形态学的方法对其进行分析发现，其中一个单系群在形态鉴定和形态测量上同其他几个有着显著的区别。因此，我们建议将Dipus分为两个种，包括四个系统发育组：D. deasyi（Deasyi组）和D. sagitta（Sagitta组、Sowerbyi组、Turanicus组）。过去的亚种D. s. deasyi提升为种；新的D. sagitta内的分类有待更多的形态数据加入进行验证。此外，皮毛颜色因表现出显著的季节性和年龄的差别，因此不适合作为亚种的形态鉴定特征；体型和头骨大小需要测量大量的标本样本才能得出具有统计学意义的显著而可信的结果。在鉴定Dipus属内的种或亚种时，地理分布应当是被首先考虑的，因为其生境的间断分布是有力的鉴别特征。我们还发现三趾跳鼠在相对湿润和高海拔地区有体型增大的趋势，而在相对干旱的地区则有相对较长的附属部位和更大的听泡。接下来，我们对三趾跳鼠的演化历史和亚洲内陆干旱区地质历史和环境变化的关系进行探索。在上一步系统发育关系的基础上，我们通过化石校正进行物种分化时间的推算，利用中性检验、错配分布和扩展贝叶斯天空曲线检测其种群历史动态，利用地理障碍分析模拟遗传格局同地理隔离的关系。我们的研究表明，三趾跳鼠的进化历史见证了亚洲内陆晚中新世以来干旱化和随后上新世造山运动导致的荒漠化的历史进程。造山运动和环境变化将整个亚洲内陆分割成数块不同的区域，三趾跳鼠的祖先受区域干旱化和地质运动的影响，而分化出数个支系。荒漠化的历史动态同三趾跳鼠遗传分化与谱系地理格局的形成息息相关。大型山系（如天山）和重要气候分界线（如200mm等降水量线）是造成支系间遗传障碍的主要因素。造山历史表现出显著的隔离效应，早期的支系分化一般与高山隆升相关。随后的多样化过程中，反复的环境变化可能造成适宜生境的片段化导致遗传分化，进而通过长时间生态分化的作用使遗传分化得到加强。种群动态分析支持不同的支系经历了不同的种群动态历史；然而，气候动荡期间持续的种群扩张和增长可能与造山运动导致的干旱化的加剧更相关。本研究以亚洲内陆干旱区的三趾跳鼠属为研究对象，通过整合分类和谱系地理的方法，整合分子和形态数据，厘清了该类群的分类问题，揭示了该类群进化历史和当前格局形成的机制，探究了亚洲内陆干旱区的地质历史和气候变化过程同该地区物种演化的关系。三趾跳鼠属应分为两个种，包括四个系统发育组：D. deasyi（Deasyi组）和D. sagitta（Sagitta组、Sowerbyi组、Turanicus组）。分子数据分析反映了长期以来被忽视的荒漠地区潜在的多样性，促进物种的有效鉴定。大型山系（如天山）和重要气候分界线（如200mm等降水量线）是造成种或亚种间遗传障碍的主要因素。气候动荡期间持续的种群扩张和增长可能与造山运动导致的干旱化的加剧更相关。 |
| 英文摘要 | Species is the basic unit and center in evolutionary research. To associate integrative taxonomy with phylogeography can not only study species evolutionary history and distribution pattern, but also clarify the traditional taxonomic system, identify samples and uncover the existence of cryptic species. Recent research about biodiversity and phylogeography in desert areas of North America, Australia and North Africa showed that desert areas were not always badlands; furthermore, species from the desert areas generally own particular evolutionary history and distribution pattern. Arid zones in Inland Asia are located in the central region of Eurasian continent which is far from the oceans; it characters with alternate huge mountains and great basins, discontinuous deserts, wavy plateau, and desert grassland. Comparing with Europe and North America in the same latitude, the complex geological history since Neocene and Pleistocene climate oscillation distinctively shaped the arid zones in inland Asia. Therefore, the evolutionary history process of the species in this area also present significant regional characteristics.Dipus is widely distributed in the arid zone in Inland Asia. It has one of the largest geographical ranges among Palearctic desert rodents, which is a suitable candidate for inferring the influence of historical geological events and climatic changes on phylogeographic patterns of this area. However, with the increasing research of Dipus, domestic and foreign scientists found a lot of taxonomic mistake in historical study. Therefore, the aim of our study is to use Dipus as an example, to systematically explore how the complex geological history and climate oscillation in arid zones in inland Asia shaped the species divergent pattern and modern distribution in spatio-temporal scale, and to search a universal regularity of the species evolutionary history in this region. In the meanwhile, we used the integrative taxonomy and phylogeography methods to clarify taxonomic problems in this taxon and to provide new sight for the desert biodiversity study. Firstly, we constructed the phylogenetic relationship and reassessed taxonomic status within Dipus. Through sampling among the major distribution areas and typical localities of different subspecies, and downloading sequences from GenBank, we totally collected 383 samples with two mtDNA (1174 bp) and six nDNA (5561 bp). We also collected body size indices from 174 individuals, skull indices from 152 individuals and skull images from 191 individuals. All specimens came from the Institute of Zoology of the Chinese Academy of Sciences (IOZCAS), the Zoological Museum of Moscow State University (ZMMSU), the Zoological Institute of the Russian Academy of Sciences in Saint Petersburg (ZISP), and the Natural History Museum (London). We used a “candidate species approach” with the divergent mtDNA phylogenetic groups and subspecies identified in a previous study as the starting point, built the phylogenetic relationship based on Bayesian and Maximum Likelihood methods, and analyzed the candidates using five species-delimitation methods and two validation methods. Dipus was long-term considered the least divergent in the Dipodinae phylogenetic line and monotypic, including only the northern three-toed jerboa, Dipus sagitta (Pallas, 1773). However, our findings indicate that mtDNA phylogenetic tree clustered four monophyly with high support, and genetic distance among them could reach 10%. The species delimitation analyses identified 5-15 species. Based on the four monophyly, we used traditional morphological statistics and geometric morphometric methods and found significant difference in one of the monophyly. Therefore, we suggest that Dipus can be divided into four phylogenetic groups that include two species: the Deasyi group (D. deasyi); Sagitta group, Sowerbyi group and Turanicus group (D. sagitta). The status of old subspecies D. s. deasyi should be species D. deasyi. The status within D. sagitta needs more morphological data to identify. According to the morphological analyses and the examined specimens, pelage color varies significantly with season and age, making it unsuitable as a diagnostic characteristic of the subspecies. Furthermore, measurements of body size and skull size require a large number of specimens to reach statistical significance and obtain reliable results. Geographical distribution should be considered first when identifying species or subspecies due to the disjunct habitats of Dipus. Our molecular analyses revealed the long-neglected potential diversity in arid regions and improved the efficiency of species/subspecies identification. We also found that individuals from more humid areas or higher altitudes were larger, whereas individuals from drier areas possessed longer appendages and larger tympanic bulla.Then, we explored the relationship between evolutionary history of Dipus and the geological history and climate change of arid zones in Inland Asia. Based on the phylogenetic tree in last section, we estimated the divergent time by fossil calibration, used neutral test, mismatch distribution and extended Bayesian skyline plot to detect demographic dynamics, and simulated correlations between geographic isolation and genetic patterns. The present study suggests that the evolutionary history of Dipus has witnessed aridification since the Late Miocene and the subsequent desertification of Inland Asia caused by the uplift of the QTP since the Pliocene. Orogenic and environmental changes separated the Inland Asia region into several distinguishable areas, and the ancestors of Dipus were affected by regional aridification as well as these geological events; thus, they diverged into different clades. The historical dynamics of desertification coincided with the genetic divergence and phylogeographic patterns of Dipus. Great mountains (such as the Tianshan Mountains) and important climate dividing lines (such as the 200 mm isohyet) were inferred to represent genetic barriers among the clades. The orogenic history showed significant isolating effects, and early clade divergence was generally related to the uplift of high mountains in the geologic history. During subsequent diversification, repeated environmental changes might have generated suitably fragmented habitats to induce genetic differentiation, which was then further reinforced and accentuated by ecological divergence over time. The demographic analyses suggested different demographic histories in distinct clades; however, the continuous expansion during the climate oscillation period appeared to be more closely related to the increasing aridification caused by orogenic movement than to climate oscillation.The present study was based on the Dipus in arid zone in Inland Asia; through the combination of integrative taxonomy and phylogeography methods, and the combination of molecular and morphological data, we clarified the status problems within this taxon, explained the mechanisms of evolutionary history and formation of modern distribution pattern, explored the relationship between geological change and species evolution. Dipus can be divided into four phylogenetic groups that include two species: the Deasyi group (D. deasyi); Sagitta group, Sowerbyi group and Turanicus group (D. sagitta). The molecular data revealed the long term ignorantly potential biodiversity in desert regions and promote the valid identification of species. Great mountains (such as the Tianshan Mountains) and important climate dividing lines (such as the 200 mm isohyet) were inferred to represent genetic barriers among the clades. The continuous expansion during the climate oscillation period appeared to be more closely related to the increasing aridification caused by orogenic movement than to climate oscillation. |
| 中文关键词 | 亚洲内陆干旱区 ; 三趾跳鼠 ; 整合分类及分类重估 ; 谱系地理 ; 系统发育 |
| 英文关键词 | Arid Zone in Inland Asia Dipus Integrative Taxonomy and Taxonomic Reassessment Phylogeography Phylogeny |
| 语种 | 中文 |
| 国家 | 中国 |
| 来源学科分类 | 动物学 |
| 来源机构 | 中国科学院动物研究所 |
| 资源类型 | 学位论文 |
| 条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/288095 |
| 推荐引用方式 GB/T 7714 | 程继龙. 三趾跳鼠（Dipus，Dipodinae，Dipodidae）系统发育、 分类重估和谱系地理学研究[D]. 中国科学院大学,2018. |
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