Knowledge Resource Center for Ecological Environment in Arid Area
| 亚洲中部干旱区敏麻蜥的系统分类和谱系地理学研究 | |
| 其他题名 | Phylogenetic systematics and phylogeography of the Steppe Racerunner (Eremias arguta) in the arid Central Asia |
| 龚雄 | |
| 出版年 | 2018 |
| 学位类型 | 硕士 |
| 导师 | 郭宪光 |
| 学位授予单位 | 中国科学院大学 |
| 中文摘要 | 摘 要 亚洲中部干旱区（Arid Central Asia，ACA）地处于欧亚大陆腹地，是世界重要的干旱区之一，具有世界干旱区最为丰富的种质与基因资源，也是世界干旱区生物多样性研究的关键区域。亚洲中部干旱区的形成和演化是第三纪以来最重要的地质历史事件之一，而干旱化起源、演化过程与第三纪以来全球剧烈的地质和气候变化的影响有关。特别是从第四纪开始，全球气候出现了明显的冰期和间冰期交替循环，伴随着冰期-间冰期旋回，沙漠面积出现动态扩张和收缩，也对现代生物区系的地理分布格局和遗传结构产生了极为深刻的影响。但是，迄今为止，亚洲中部干旱区荒漠动植物居群动态变化、物种进化历史和地理分布的研究仍然很缺乏。敏麻蜥是麻蜥属在欧亚大陆分布最广的物种之一，其分布区横贯整个欧亚大陆，分布主体为亚洲中部干旱区，属于典型的耐干旱物种，是研究亚洲中部干旱区时空演化对种群遗传分化和群体动态影响的理想材料。目前关于敏麻蜥的研究主要集中在基于形态学的分类，而关于其物种进化、遗传结构和谱系地理格局的形成等的研究相对较少。本研究通过联合形态和分子数据、采用线粒体基因和多个核基因标记、并且引入物种分布模型，对敏麻蜥的遗传结构和种群历史动态进行研究，旨在揭示敏麻蜥的谱系地理格局、各支系间的分歧时间及起源与演化，解析冰期-间冰期旋回对敏麻蜥种群动态的影响，以及解决一些种下分类问题。主要研究结果如下： 1. 新疆博乐和伊犁河谷敏麻蜥的种下分类地位探讨 采用形态比较和基于线粒体细胞色素b（Cyt b）基因序列的分子系统发育分析，对新疆博乐和伊犁河谷的敏麻蜥4个种群、28号样本进行种下分类地位探讨。联合GenBank中的敏麻蜥细胞色素b基因序列，采用最大简约法、最大似然法和贝叶斯推断法构建系统发育树进行亚种界定。采用贝叶斯因子，通过比较限制性和非限制性贝叶斯树的拓扑结构来检验有关敏麻蜥亚种分类的几种相互竞争的假设。结果表明，博乐种群的形态特征与伊犁河谷的敏麻蜥一致，雄性的背侧在繁殖季节有醒目的蓝色或绿色眼点。系统进化树也一致表明来自博乐的单倍型属于伊犁河谷支系，为一个尚未描述的分类群（Eremias arguta ssp.）。以往有关伊犁河谷种群属于指名亚种（E. a. arguta）或东方亚种（E. a. potanini）或乌兹别克斯坦亚种（E. a. uzbekistanica）的观点均被显著拒绝。伊犁河谷支系最有可能与乌兹别克斯坦亚种和伊塞克湖亚种（E. a. darevskii）二者构成的支系形成姐妹群，但并没有强的证据拒绝备择假说即伊犁河谷支系位于树的基础位置与其余支系形成姐妹群。此外，重建的系统发育树中指名亚种与东方亚种形成了交互单系，尽管自展支持率很低且后验概率不高；其备择假设即“东方亚种”嵌在指名亚种支系中，也没有很强的证据而拒绝。总之，博乐的敏麻蜥种群不属于东方亚种，而隶属于一个单独的伊犁河谷支系（E. arguta ssp.）；伊犁河谷的敏麻蜥种群不应该划分为指名亚种、东方亚种或乌兹别克斯坦亚种，而是属于尚未描述的新亚种；伊犁河谷这一支系的系统发育位置还不明确，需要采用整合分类学的方法来澄清。此外，结合形态变异，还讨论了东方亚种的有效性。 2. 基于线粒体DNA的敏麻蜥种群遗传结构和种群动态研究 通过PCR扩增和测定了敏麻蜥81个样点，共349号个体的Cyt b基因序列（1143 bp），联合GenBank中Cyt b基因序列共61条，一起用于分子系统发育分析。所有线粒体Cyt b分子数据共识别出了183个单倍型，基于单倍型构建的MP、BI和ML系统发育树拓扑结构基本一致，特别是ML树和BI树拓扑结构几乎完全一致。三种方法所得到的进化树均支持敏麻蜥形成一个单系（MP/ML/BI: 100％/100％/1.0），并识别出8个明显的分支（Clade I–Ⅷ），也与八个地理单元相对应，其中6个分别与传统上基于形态划分的亚种相对应：敏麻蜥东方亚种（E. a. potanini）、指名亚种（E. a. arguta）、外高加索亚种（E. a. transcaucasica）、西方亚种（E. a. deserti）、乌兹别克斯坦亚种（E. a. uzbekistanica）、伊塞克湖亚种（E. a. darevskii），另外两个支系分别为采自中国和哈萨克斯坦伊犁河谷地区的伊犁河谷支系（E. arguta ssp.1）和采自哈萨克斯坦卡拉套山地区的卡拉套山支系（E. arguta ssp.2）。总体而言，基于分子系统发育研究的结果与形态学分类部分一致，一定程度上支持了东方亚种的有效性，并发现二个新的隐存支系，即伊犁河谷支系和卡拉套山支系。这种谱系地理格局也得到了遗传距离分析、系统发育网络图分析、分子变异分析（AMOVA）和单倍型网络图分析（Network）的支持。我们推测，敏麻蜥分布范围广泛，不同地理种群的变异很大，更多的隐存支系有待识别。鉴于这两个支系在形态和分子方面与其他亚种均具有明显的区别，建议将其划分为新的亚种。中介单倍型网络图分析将敏麻蜥分为八大簇群，分别与系统进化树的八个支系相对应。敏麻蜥各个支系间也已经出现了较为明显的分化，不同支系间没有共享单倍型。伊犁河谷的敏麻蜥形成了一个单独的簇，星状的网终图和末梢没有共享单倍型的式样表明伊犁河谷支系近期可能有种群扩张；来自哈萨克斯坦卡拉套山的敏麻蜥形成了一个单独的簇；来自准噶尔盆地的敏麻蜥形成了一个单独的簇，星状的网终图和末梢没有共享单倍型的式样表明表明东方亚种近期可能有种群扩张。伊犁河谷两岸的敏麻蜥大体上可识别左右两个不同的亚簇，但未形成交互单系；伊犁河谷两岸的敏麻蜥之间没有共享单倍型，表明两岸种群间发生了较强的分化；与外群中介麻蜥（Eremias intermedia）近缘的单倍型全部都来自伊犁河谷左岸的种群，这表明伊犁河谷左岸的单倍型可能更为“古老”。 采用贝叶斯松散分子钟模型，采用外群标定估算出的蜥蜴科时间树结果表明敏麻蜥的最近共祖时间为4.53 Ma（95%CI：3.06-5.89 Ma）。对敏麻蜥内群的各个支系的分化时间进行估算，结果表明，伊塞克湖亚种（Clade Ⅵ）和乌兹别克斯坦亚种（Clade V）与其他亚种的共祖时间约为3.55 Ma （95%CI：2.12-4.90 Ma）；伊犁河谷支系（Clade Ⅶ）与东方亚种、指名亚种、卡拉套山支系、外高加索亚种和西方亚种所构成的大支（Clade I-IV、Ⅷ）共祖时间约为3.69 Ma（95%CI：2.38-5.17Ma）；西方亚种（Clade IV）与东方亚种、指名亚种、卡拉套山支系和外高加索亚种所构成的大支（CladeI-Ⅲ、Ⅷ）共祖时间约为2.57 Ma（95%CI：1.52-3.64Ma）；卡拉套山支系（Clade Ⅷ）与东方亚种、指名亚种（Clade I-Ⅱ）共祖时间约为1.467 Ma（95%CI：0.83-2.14 Ma）；东方亚种（CladeI）和指名亚种（CladeⅡ）共祖时间约为0.38 Ma（95%CI：0.20-0.55 Ma）。这些时间节点与亚洲中部干旱区的在上新世以来干旱化加强趋势相一致。 对敏麻蜥东方亚种（Clade I）、指名亚种（Clade II）、西方亚种（Clade IV）和伊犁河谷支系（Clade Ⅶ）四个支系分别进行种群历史动态分析。中性检验（Tajima’s D与Fu’s FS）和错配分布分析（mismatch distribution）支持东方亚种在历史上种群经历了扩张；而指名亚种、西方亚种在历史上种群可能保持稳定；中性检验支持伊犁河谷支系经历了近期的种群扩张。贝叶斯轮廓图表明东方亚种在LGM时期有效种群大小出现了轻微的下降，而约5 ka以来，有效种群大小出现了快速增长；指名亚种在LGM时期有效种群大小出现了轻微增长，而约12 ka以来，种群大小出现了快速下降；西方亚种在LGM时期有效种群大小出现了轻微增长，而约2.8 ka以来，种群大小出现了一定的下降；伊犁河谷支系在LGM时期有效种群大小基本处于恒定状态，而约11 ka以来，种群大小出现了快速增长。 生态位模拟发现敏麻蜥的四个亚种或支系（指名亚种、东方亚种、西方亚种和伊犁河谷支系）对冰期的响应模式具有支系特异性：敏麻蜥东方亚种、指名亚种和西方亚种的分布区在冰盛期（LGM）扩张，在间冰期（LIG）收缩，符合GM扩张模型；伊犁河谷支系的分布区在冰盛期（LGM）收缩，在间冰期（LIG）扩张，符合GM收缩模型。 针对敏麻蜥对未来2050s（2041-2060年）和2070s（2061-2080年）两个时间段4种气候排放情景下的分布区进行模拟，均显示敏麻蜥伊犁河谷支系在伊犁河谷中部的生境在逐步丧失，伊犁河谷支系未来的分布在向伊犁河谷的两侧扩张。我们推测，这可能是与伊犁河谷独特的地理环境有关。随着全球气候变暖，导致伊犁河谷两侧的雪山冰雪融化，雪线上升，而敏麻蜥的分布可以达到海拔1800m左右，雪线上升暴露出的地区很适合敏麻蜥生存；同时，因为冰雪融化，导致大量雪水进入伊犁河谷，使得伊犁河两岸变得湿润，而敏麻蜥更喜好干旱环境，这也迫使敏麻蜥向伊犁河谷两侧更高海拔的地区迁移。最终导致敏麻蜥伊犁河谷支系未来分布区扩大。 3. 基于核基因的谱系地理结构初步分析 通过PCR扩增和测定了敏麻蜥81个样点，共349号个体的八个核基因PRLR（prolactin receptor）、KIF24（kinesin family member 24）、CGNL1（cingulin-like 1）、β-fibint7、EXPH5（exophilin 5）、MKL1（megakaryoblastic leukemia 1）、MAP1A （microtubule-associated protein 1A）、UBN1（ubinuclein 1），共筛选扩增出了321号个体KIF24（561bp），336号个体CGNL1（903bp），307号个体β-fibint7（675bp），315号个体EXPH5（984bp），307号个体MKL1（1050bp），325号个体PRLR（546bp），320号个体UBN1（741bp），313号个体MAP1a（1803bp），每个支系都扩增出了相应的八个核基因的代表。利用核基因分别构建BI和ML树，结果并没有显示出与线粒体基因相同支系结构。每个核基因分别构建单倍型网络图，也没有显示出明显的谱系群结构。核基因与线粒体基因结果的不一致，我们认为可能与核基因较为保守，进化速率慢，而有效种群更大，容易引起不完全谱系分选有关。 |
| 英文摘要 | AbstractArid Central Asia (ACA) is located in the interior of Eurasia, which is one of the most important arid regions with richest germplasm and genetic resources, and is a key area for studying biodiversity evolution in the world’s arid region. Its formation and evolution is one of the most important geological and historical events, being clolsely related to the dramatic global climatic and geological changes since the Tertiary. In particular, during the Quaternary, the global climate experienced significant glacial and inter-glacial cycles, accompanied by the dynamic expansion and contraction of desert areas, which imposed profound effects on the geographical distribution pattern and genetic structure of modern biota. However, until recently, the studies on the dynamic changes of populations, evolutionary history and geographical distribution of flora and fauna in the ACA have been lacking. Eremias arguta is one of the most widely distributed species in the Eurasian continent, which transverses the entire Eurasia and mainly occupies the areas of ACA. E. arguta is also a typical drought-tolerant species and is an ideal organism to study the potential influence of ACA transformation on the population genetic differentiation and historical demography. At present, the studies about E. arguta mainly focus on the classification based on morphology. However, there are relatively few studies on its genetic differentiation, phylogeographical pattern, and evolutionary history. In this study, by combining morphological and molecular data (mitochondrial and multiple nuclear gene markers) as well as ecological niche modeling analyses, we aim to estimate the phylogeographical structure and divergence times between the major lineages of E. arguta. Furthermore, we are to explore the population dynamics of some major lineages of E. arugta in response to the glacial and inter-glacial cycles during the Quaternary. In addition, we will assess some issues on intraspecific taxonomy. The main results are as follows.1. On intraspecific taxonomy of E. arguta populations from Ily River Valley and Bole City, Xinjiang Uyghur Autonomous Region.We performed morphological analyses and phylogenetic reconstruction using mitochondrial Cyt b gene to address the status of intraspecific taxonomy of 28 individuals from 4 populations in the Ily River Valley and Bole City, Xinjiang. In combination with the sequences of Cyt b downloaded from GenBank, we reconstructed the phylogeny of E. arguta with Maximum Parsimony (MP), Maximum Likelihood (ML), Bayesian Inference (BI). Bayes factors were used to compare the unconstrained Bayesian tree topology to Bayesian trees with ‘hard’constraints to test the competitive hypotheses about the subspecies status in E. arguta. Our results showed that lizards from Bole City and Ily River Valley exhibit consistent morphological characters, with distinct blue or green ocelli on lateral dorsal of male during breeding season. All phylogenetic analyses indicated that the haplotypes from Bole City were nested within the Ily River Valley clade, which is an undescribed taxon, Eremias arguta ssp. Although these results explicitly rejected the hypothesis that populations from the Ily River Valley belong to E. a. arguta, E. a. potanini, or E. a. uzbekistanica, basal split of the Ily River Valley clade cannot be rejected significantly. E. a. arguta and E. a. potanini formed reciprocal monophyly albeit with weak support on each node. The hypothesis that E. a. potanini was nested within E. a. arguta was rejected by Bayes factors. It is necessary to clarify the status of the Ily River Valley clade by using the integrative taxonomic approach. In addition, in combination with morphological differentiation, the validity of E. a. potanini was discussed.2. Population diversification and historical demography of E. arguta based on MtDNA.We amplified and sequenced mitochondrial cyt b (1143 bp) gene of 349 individuals from 81 localities. In combination with 61 cyt b gene sequences of E. arguta downloaded from GenBank, we produced 183 haplotypes. Phylogenetic reconstruction by MP、BI and ML approaches obtained overall consistent topologies; especially ML and BI trees were almost identical. All analyses supported the monophyly of E. arguta and recovered eight distinct, biogeographically discrete, and well-supported clades (Clades I–VIII), revealing genetically identifiable populations corresonding to some preveioulsy morphology-defined subspecies, i.e. E. a. potanini, E. a. arguta, E. a. transcaucasica, E. a. deserti, E. a. uzbekistanica, E. a. darevskii, E. arguta ssp.1 (Ily River Valley populations) and E. arguta spp.2 (Karatau populations), respectively. The phyographical structure was supported by AMOVA and NETWORK analyses. We infer that the Clade VIII consisting of the population in Karatau belongs to an undescribed subspecies.Median-joining network analyses yieled eight clusters corresponding to the eight clades, respectively. No haplotype was shared between different clades, suggestive of apprarent differentation among the clades. The samples from Ily River Valley formed a distinct cluster, which star-like shape and lack of shared haplotype in tips implied recent populaton expansion. The samples from Karatau in Kazakhstan also formed a distinct cluster. The samples from Junggar Basin formed a distinct cluster, which star-like shape and lack of shared haplotype in tips implied recent populaton expansion. Overall, two subclusters could be recognized in view of the left and right banks of the Ily River. Similar to the phylogentic tree, the two subclusters did not form reciprocal monophyletic group. There was no shared haplotype between the two banks, suggestive of apparent genetic differentiation. Those haplotypes which are closely related to the outgroup Eremias intermedia were all located on the left bank. These pattern indicated that the haplotypes from the left bank may be more ancestral.Bayesian relaxed molecular clock analyses indicated that the MRCA (most recent common ancestor) of E. arguta was at 4.53 Ma (95% CI：3.06-5.89 Ma). Clade VI (E. a. darevskii) and VII (E. a. uzbekistanica) diverged with all other subspecies at 3.55 Ma (95% CI：2.12-4.90 Ma). Clade V (E. arguta ssp.) diverged from those including Clade I-IV (E. a. potanini, E. a. arguta, E. a. transcaucasica and E. a. deserti) at 3.69 Ma (95% CI：2.38-5.17 Ma). Clade IV (E. a. deserti) diverged from those including Clade I-III (E. a. potanini, E. a. arguta and E. a. transcaucasica) at 2.57 Ma (95% CI：1.52-3.64 Ma). Our results suggest that the intensified aridifications from the Pliocene onwards drove the diversification of E. arguta in general.We conducted historical demographic analyses for E. a. potanini (Clade I), E. a. arguta (Clade II), E. a. deserti (Clade IV) and E. arguta ssp.1 (Clade VII). Neutral tests (Tajima’s D与Fu’s FS）and mismatch distribution indicated a scenario of demographical expansion for E. a. potanini, but demographial stable for E. a. arguta and E. a. deserti. Only neutral tests supported a scenario of demographical expansion for the populations from the Ily River Valley. Analyses of data using Bayesian skyline plots suggested that: E. a. potanini had undergone a weak decline during LGM, but a rapid growth since 5 ka; E. a. arguta had undergone a weak growth during LGM, but a rapid decrease since 12 ka; E. a. deserti had undergone a weak growth during LGM, but somewhat a decline since 2.8 ka; the Ily River Valley clade showed a stable condition in terms of the effective population size, along with a rapid growth since since the beginning of the Holocene (~11 ka).Ecological niche modeling analyses implicated a significant role of both the LIG and LGM in shaping the demographic history of the Steppe Racerunner and reveal lineage- specific response to Pleistocene climate fluctuations in the species. For E. a. potanini, E. a. arguta and E. a. deserti, their potential distribution range expanded during LGM, and contracted during LIG, consistent with the predictions of the GM expanision model. For the Ily River Valley clade, their potential distribution range contacted during LGM, and expanded during LIG, consistent with the predictions of the GM contraction model. We also conducted ecological niche modeling analyses for E. arguta ssp. to predict the present and future (2050 and 2080) distribution. Theses results indicated that the distribution of population from Ily River Valley was expanding toward the flanks of the valley during future. These phenomena may relate to the specific geography of this valley. With the global warming, snow on both sides mountains of the Ily River Valley melt, and the snow line rises. As the distribution of E. arguta can reach more than 1800 m above sea level, the areas exposed by rising snow lines may be suitable for the survival of E. arguta. At the same time, because the melting of snow on the mountains has led to a large amount of snow water entering the Ily River Valley, the two banks of the Ily River have become moist. Changes in the living environment forced E. arguta to migrate to higher elevations on both sides of the Ily River Valley, as E. arguta prefers arid environment. Eventually it led to the expansion of the future distribution area of E. arguta in the Ily River Valley.3. Preliminary phylogeography studies based on nuclear genes.Through PCR amplification and sequencing, we obtained eight nuclear genes covering 349 individuals from 81 populations, including PRLR (prolactin receptor), KIF24 (kinesin family member 24), CGNL1(cingulin-like 1), β-fibint7 (β-fibrinogen intron 7), EXPH5 (exophilin 5), MKL1 (megakaryoblastic leukemia1), MAP1A (microtubule-associated protein 1A) and UBN1 (ubinuclein 1) genes. The obtained sequences including 321 KIF24 (561 bp), 336 CGNL1 (903 bp), 307β-fibint7(675 bp), 315 EXPH5 (984 bp), 307 MKL1 (1050 bp), 325 PRLR(546 bp), 320 UBN1(741 bp) and 313 MAP1a (1803 bp) covered all eight major clades. BI and ML analyese based on eight nuclear genes didn’t produce consistent topology with the matriline reconstruction. Haplotype network based on each nuclear gene didn’t show apparent genealogy structure. The inconsistent results between nuclear and mitochondrial genes may be ascribed to more conservative, slow evolutionary rate, and larger effective population with nuclear genes which led to incomplete lineage sorting. |
| 中文关键词 | 敏麻蜥 ; 亚洲中部干旱区 ; 系统分类 ; 谱系地理学 |
| 英文关键词 | Eremias arguta Arid Central Asia (ACA) Phylogenetic systematics Phylogeography |
| 语种 | 中文 |
| 国家 | 中国 |
| 来源学科分类 | 动物学 |
| 来源机构 | 中国科学院成都生物研究所 |
| 资源类型 | 学位论文 |
| 条目标识符 | http://119.78.100.177/qdio/handle/2XILL650/288060 |
| 推荐引用方式 GB/T 7714 | 龚雄. 亚洲中部干旱区敏麻蜥的系统分类和谱系地理学研究[D]. 中国科学院大学,2018. |
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