我国东北及萨拉乌苏地区晚更新世披毛犀的演化及迁移
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摘要
真披毛犀(Coelodonta antiquitatis Blummenbach,1799)是腔齿犀属(Coelodonta Bronn,1831)的一个进步种,它是在更新世冰期气候的影响下逐步发展成为适应寒冷草原、冰缘苔原和冻土苔原生活环境的典型冰缘动物。在更新世时期,披毛犀曾广泛分布于北半球72°N至33。N的广大地区。在欧亚大陆北部广大地区内发现的披毛犀化石,绝大多数是更新世晚期的,其早期记录只有来自中国几个地点的少量化石材料。目前这个属的最早代表是发现于西藏西南部札达盆地的西藏披毛犀(Coelodonta thibetana,3.7Ma),另一个早期腔齿犀化石是发现于我国甘肃省临夏盆地的泥河湾披毛犀(Coelodonta nihowanensis,2.5Ma)。相比较而言,中国区域以外腔齿犀属(Coelodonta)化石记录出现的要晚一些,其典型代表是在俄罗斯联邦布里亚特共和国境内发现的属于中更新世早期的托洛伐伊披毛犀(Coelodonta tologoijensis,0.75Ma)。在欧洲,根据几个早期化石点(比如罗马尼亚)的化石记录,腔齿犀属(Coelodonta)最早出现于400-460ka时期。因此,一些学者认为腔齿犀属(Coelodonta)很可能起源于中国。由亚洲起源的这种腔齿犀在中更新世首次到达欧洲的东部和中部,并在第四纪冰期气候的影响下最终演化为适应寒冷草原环境的最著名的冰期动物——真披毛犀(Coelodonta antiquitatis)。真披毛犀在欧洲演化出现后,在随后寒冷、干燥的时期,它又扩散到亚洲北部和中国。由于化石记录的不完备性,特别是腔齿犀属早期化石记录的缺乏,关于披毛犀的起源、迁移、演化等问题,人们的认识还比较模糊。
1986年,随着聚合酶链式反应(PCR)技术的发明,特别是迅猛发展的分子生物学技术(多重PCR、大规模测序、高通量测序、直接多重测序、阵列序列捕获测序),使得从古代生物的遗体中提取并扩增DNA成为现实。古DNA作为遗传信息的载体,保存有生物遗传变异和生长发育的全部信息,为人们探寻漫长历史年代中生物种群系统发生与演变规律提供重要的研究资料,同时也为人们重建生物的起源与进化历程提供了一种新的研究方法。目前,古DNA技术在生物的起源、演化、迁移、遗传多样性等方面的研究中正发挥着越来越重要的作用。
从分子水平上,人们对披毛犀的古DNA研究工作开展的还非常有限。到目前为止,世界上公开报道的研究工作也非常少。Orlando等(2003)对采自比利时的披毛犀牙齿化石进行古DNA研究,他们利用所得到的完整12S rRNA和／或部分细胞色素b基因所构建的系统发育树显示,披毛犀与现生的苏门答腊犀牛亲缘关系最近。Binladen等(2006)对采自西伯利亚永久冻土中骨骼样品的线粒体DNA与核DNA基因的错配情况进行探讨。研究表明在线粒体DNA和核DNA中都存在着由于受损而遗传密码错配的情况,由胞嘧啶→胸腺嘧啶、鸟嘌呤→腺嘌呤的转换比胸腺嘧啶-→胞嘧啶、腺嘌呤→鸟嘌呤转换出现的次数多得多。这一研究结果显示,胞嘧啶的去氨基作用转变为尿嘧啶是古DNA(无论是线粒体DNA还是核DNA)错配的主要原因。Willerslev等(2009)从采自俄罗斯雅库特永久冻土中披毛犀的毛发中首次获取到披毛犀的完整线粒体基因。利用披毛犀和现生五种犀牛的线粒体基因构建的系统发育树显示,非洲的黑犀牛与白犀牛聚为一个分支,亚洲的爪哇犀牛与印度犀牛聚为一支；真披毛犀与苏门答腊犀牛聚为另一个分支。但是,根据构建系统发育树时所采用的基因不同或者选择不同的外类群,上述三个分支之间的关系就会发生变化。所以,披毛犀/苏门答腊犀牛、爪哇犀牛/印度犀牛、黑犀牛/白犀牛这三个分支之间的系统发育问题还未得到解决。
同时,Orlando等(2003)和Willerslev等(2009)还利用化石锚定点进行分子钟推算,得到披毛犀与苏门答腊犀牛的分歧时间为21-26Ma和17.5-22.8Ma,这与目前已知披毛犀的最早化石记录3.7Ma时间间隔差距较大。而且,Orlando等(2003)也指出他们关于披毛犀与苏门答腊犀牛分歧时间的计算是比较粗略的,因为基于同样化石标准进行分子钟估算,得到的结果与马属动物出现的时间不相符。所以,人们还需要做进一步的研究工作来探讨披毛犀与其近亲的分歧时间问题。
另外,Deng等(2011)为了评价西藏披毛犀(Coelodonta thibetana,3.7Ma)在犀亚科内的系统发育位置,利用17个犀牛属种：全部5种现生犀牛和12个绝灭的犀牛属种(包括已知的全部4种披毛犀：西藏披毛犀、泥河湾披毛犀、托洛戈伊披毛犀和真披毛犀)从形态学的角度进行了系统发育分析。研究结果表明苏门答腊犀牛既是两种现生独角犀牛(印度犀牛和爪哇犀牛)的姐妹群,也是披毛犀支系的姐妹群,或者两种独角犀(印度犀牛/爪哇犀牛)先与披毛犀支系形成姐妹群关系,而苏门答腊犀牛则是这个更大支系的姐妹群。而从分子水平上构建的系统发育树显示披毛犀与现生的苏门答腊犀牛亲缘关系最近。那么,这一形态学分析结论与来自分子水平的系统发育分析结果不一致。
披毛犀与现生的哪一种犀牛亲缘关系最近?披毛犀与其近亲的分歧时间?披毛犀在欧亚大陆之间的扩散时间?经历了何种扩散路线?披毛犀的绝灭等都是值得进一步研究的课题。
中国披毛犀在披毛犀的演化发展历史中占有非常重要的地位。我国发现的披毛犀化石,在地质时代上延续时间较长。在我国东北及萨拉乌苏地区保存有大量的晚更新世真披毛犀化石材料,样品来源丰富,而且这些地方气温常年偏低,也非常有利于古DNA的保存。本研究的样品采集于晚更新世地层中,不超出古DNA的理论保存年限10万年,这些都为披毛犀古DNA研究工作的顺利开展提供了很好的研究材料。到目前为止,在我国萨拉乌苏及东北地区存在有大量晚更新世披毛犀化石的情况下,对该地区晚更新世披毛犀化石材料的古DNA研究开展的还非常有限。
本研究利用采自我国内蒙古自治区的萨拉乌苏、黑龙江省的青冈和肇东地区晚更新世八个披毛犀骨骼样品材料(分别距今大约42000年、39000年和35000年),提取得到部分或完整披毛犀线粒体细胞色素b基因,不仅丰富了披毛犀的基因库,而且使人们了解我国不同地点、不同年代披毛犀的基因分异度。调集GenBank中披毛犀的同源序列以及现生犀牛序列,重建披毛犀的分子系统发育演化树,提高中国披毛犀系统演化分辨率。另外,本研究利用分子钟探讨了披毛犀与苏门答腊犀牛的分歧时间。首先利用外类群化石记录为锚定点,即马科动物和角型亚目的分歧时间(56Ma)、偶蹄目和鲸类的分歧时间(60Ma)为基准,利用MEGA4.0软件来推算披毛犀与现生的苏门答腊犀牛的分歧时间。基于化石记录马科动物和角型亚目的分歧时间56Ma,利用BEAST1.6.1软件贝叶斯马尔科夫链蒙特卡洛(MCMC)算法估算披毛犀与苏门答腊犀牛的分歧时间。其次,采用Network4610软件,基于细胞色素b基因的进化速率为2%/百万年来计算披毛犀与苏门答腊犀牛的分歧时间。此外,本研究还结合第四纪气候的变化,探讨披毛犀的欧亚迁移。
主要得到以下几点结论：
(1)从采自我国东北及萨拉乌苏地区八个披毛犀骨骼化石材料中,获取到84-1140bp长度不等的细胞色素b基因。其中肇东样品C.a._HS14得到完整细胞色素b基因,另一肇东样品C.a._HS12也得到长度为1130bp的细胞色素b基因片段,C. a._Qg13获得总共490bp的细胞色素b基因片段；C. a.SL1获得651bp的细胞色素b基因片段；C. a._SL4获得总长1100bp的细胞色素b基因片段。以上五个样品所获得的基因序列已提交GenBank, GenBank收录号分别为：GU371439、GU371440、JQ974919、JQ974920、 JQ974921。另外三个样品所获得的序列相对较短,青冈样品Cα._Qgll获得84bp的细胞色素b基因片段；青冈样品C. a._Qg14获得140bp的细胞色素b基因片段；萨拉乌苏样品C. a._SL5获得204bp的细胞色素b基因片段。重复性实验在哥本哈根大学的古DNA研究中心进行,证明本研究所得到的披毛犀序列是真实、可靠的。
(2)从我国东北及萨拉乌苏地区晚更新世披毛犀化石材料中提取到古DNA基因,说明我国萨拉乌苏及东北地区的土壤、气候环境条件比较适合于古DNA的保存。但从研究结果来看,这些样品的保存状况不及比利时洞穴和西伯利亚永冻土中真披毛犀样品保存的好,而且即使是同一地点、同一地层中的不同样品,保存状况也有较大差异。
(3)无论是用MEGA软件还是采用贝叶斯分析方法,所构建的分子系统发育树均显示所有的披毛犀样品都聚为一支,这反应其序列的同源性,且披毛犀与现生的苏门答腊犀牛亲缘关系最近。另外,从所构建的分子系统发育树还显示出,采自内蒙古自治区萨拉乌苏的样品(C. a._SL1、C. a._SL4、C. a._SL5)与一个黑龙江省肇东地区的样品(C a._HS14)聚为一个分支,采自黑龙江省肇东和青冈地区的其它样品(C. a._HS12、C. a._Qg13)与来自欧罗斯雅库特的样品(C. a_Willerslev)聚在一起,说明在晚更新世我国萨拉乌苏及东北地区的披毛犀与雅库特地区的披毛犀存在着基因交流,它反映了在第四纪冰期／间冰期的交替过程中,随着气候的变化,披毛犀这种典型的冰缘动物由北向南或由南向北的迁移。
(4)本研究采用两种分子钟方法来计算披毛犀与苏门答腊犀牛的分歧时间。首先,基于外类群中化石记录作为校正标准,利用MEGA软件系统发育分析推算出披毛犀与苏门答腊犀牛在24.5-27.6Ma产生分歧,利用BEAST软件进行系统发育分析推算出披毛犀与苏门答腊犀牛在22.5Ma产生分歧。其次,根据细胞色素b基因演化速率2%／百万年,利用Network软件推算出披毛犀与苏门答腊犀牛的分歧时间为3.8-4.7Ma。对于这两种分子钟方法推算出的两种分歧时间刻度,笔者认为利用外类群中已知化石的分歧时间来进行分子钟估算,得到的较老的分歧时间刻度高估了两者的分歧时间,而认为基于细胞色素b基因2%/百万年演化速率推算出的较近的分歧时间刻度较为可信,并且该分歧时间也与目前所知最早腔齿犀化石材料的年代相吻合。
(5)本研究中所获得不同地点、不同年代披毛犀的基因序列与GenBank中披毛犀序列相比较,发现在晚更新世披毛犀的遗传分异度比较低,或许遗传多样性的缺失是导致其绝灭的原因之一。比较不同地区披毛犀的基因分异度,结果显示我国萨拉乌苏地区披毛犀的遗传分异度最高,其次是我国东北地区。综合不同地区之间的情况来看,我国东北与雅库特和西伯利亚样品之间的基因分异度最低：我国东北与萨拉乌苏地区样品之间的基因分异度相对较高。
Woolly rhinoceros (Coelodonta antiquitatis Blummenbach,1799), an improvement species of Coelodonta(Coelodonta Bronn,1831), was highly adapted to the environment on cold grassland, periglacial tundra and permafrost tundra, which was gradually developed into a typical periglacial animal in the influence of Pleistocene glacial climate. During the Pleistocene, woolly rhinoceros was widely distributed in the Northern Hemisphere from72°N to33°N. The extensive woolly rhinoceros fossil records were found in northern Eurasia, but most of them belong to late Pleistocene. The early fossil records of the genus have been founded in several sites from China and the amount of early fossil materials is very limited. Up to now, the earliest representative of the genus, Coelodonta thibetana (3.7Ma), was found in the Zanda Basin in southwestern Tibet. Another early fossil record, Coelodonta nihowanensis (2.5Ma), was found in the Linxia Basin in Gansu Province, China. Comparably, the earliest fossil species outside China appeared later than that from China. A typical representative, Coelodonta tologoijensis (0.75Ma), has been found around the early middle Pleistocene in Buryatia, Russian Federation. In Europe, Coelodonta first appeared around400-460ka according to several early fossil records (such as Romania). Therefore, some researchers suggested that the woolly rhinoceros (Coelodonta) may have originated in China. After the origination of this genus in Asia, it diffused to eastern and central Europe in the middle Pleistocene for the first time, and gradually evolved to adapt the life on the cold tundra and steppe in the influence of Quaternary glacial climate, and it finally evolved into the most famous ice age animal——the true woolly rhinoceros (Coelodonta antiquitatis). After the origination of this species in Europe, it dispersed to north Asia and China in the following cold and dry period. Due to the incompleteness of the fossil record, especially the lack of early fossil records and very limited sampling sites, our understanding on its origin, migration, evolution and other issues is very ambiguous.
In1986, with the invention of polymerase chain reaction (PCR) technology, especially the rapid development of molecular biology technology (multiple PCR, large scale sequencing, high throughput sequencing, direct multiplex sequencing, array-based sequence and so on), the extraction and amplification of DNA from ancient biological remains come true. Ancient DNA, as the carrier of genetic information, contains all the information of biological genetic variation and growth. It could provide important research data for people to explore the occurrence of biological system and evolution during the long history. At the same time, it also provides us a new research method to rebuild the origin and evolution process of life. So ancient DNA technology is playing more and more important role in the the study of origin, evolution, migration and genetic diversity of life.
At the molecular level, the study on woolly rhinoceros is very limited. Until now, there are only several cases reported in the world. Orlando et al.(2003) extracted complete12S rRNA gene and partial cytochrome b gene of woolly rhinocers collected from Belgium. Based on the sequences, they performed the phylogenetic analyses and the results indicated that woolly rhinoceros is more closely related to extant Dicerorhinus sumatrensis. Binladen et al.(2006) investigated the frequency and types of miscoding lesions in mtDNA and nuDNA marks using two woolly rhinoceros permafrost bone samples, suggesting that there was no significant evidence for nuDNA sequences being more prone to miscoding lesions than mtDNA sequences, the conversion ratio from cytosine into thymine and from guanine into adenine occured more rates than that from Thymine into cytosine and from adenine into guanine. This study indicated that the deamination from cytosine into uracil is the main mismatch in ancient DNA ((both mitochondrial DNA and nuclear DNA). Willerslev et al.(2009) first obtained the whole mitochondrial genome sequences of woolly rhinoceros collected from permafrost inYakutia, Russian. Using the obtained mitochondrial DNA of woolly rhinoceros together with five extant rhino mitochondrial genome sequences, phylogenetic analysis was performed and the results indicated that the six species clustered into three sister groups:Diceros bicornis ICeratotherium simum, Rhinoceros sondaicus/Rhinoceros unicornis, Coelodonta antiquitatis I Dicerorhinus sumatrensis. However, the rhinoceros phylogenetic trees are highly diffuse, the relationship between the three branches will change when using different genes or different out groups. So, the phylogenetic issue between Coelodonta antiquitatis/Dicerorhinus sumatrensis, Rhinoceros sondaicus/Rhinoceros unicornis, Diceros bicornis ICeratotherium simum has not been resolved.
Orlando et al.(2003) and Willerslev et al.(2009) carried out the molecular clock calculations based on the calibration time points of out groups, and they obstained the divergent timescales21-26Ma and17.5-22.8Ma for woolly rhinoceros from Sumatran rhinoceros, there is a big gap between these timescales and the known earlist fossil record of woolly rhinoceros. Moreover, Orlando et al.(2003) also pointed out the evolutionary timescale for woolly rhinoceros from Sumatran rhinoceros should be taken as preliminary because the same calibration failed to recover the date of emergence of the Equus genus. So, people need to do further researches to explore the divergence time between woolly rhinoceros and its relatives.
In addition, to investigate phylogenetic status of Coelodonta thibetana (3.7Ma), Deng et al.(2011) reconstructed phylogenetic trees based on the morphological data, using seventeen rhinoceros genera which contained all the five extant rhinoceros and twelve extinct rhinoceros (including all the known extinct Coelodonta:Coelodonta thibetana, Coelodonta nihowanensis, Coelodonta tologoijensis and Coelodonta antiquitatis). The results show that Dicerorhinus sumatrensis clustered together with two extant one-horned rhinoceros (Rhinoceros sondaicus/Rhinoceros unicornis) to form a sister group, it also formed a sister group with the branch of Coelodonta, or two extant one-horned rhinoceros first clustered together with the branch of Coelodonta, and then Dicerorhinus sumatrensis formed a sister group with the larger branch. However, at the molecular level, the the phylogenetic trees showed that woolly rhinoceros is most closely related to one of the extant rhinoceros species, Sumatran rhinoceros, and this result was inconsistent with the study based on morphological data.
Which extant rhinoceros is more closely related to woolly rhinoceros? When did woolly rhinoceros separate from its relatives? When did Coelodonta diffuse from Asia to Europe? What routes did it experience during the process of migration? And other issues such as its extinction also need further exploration.
Woolly rhinoceros remains from China occupy a very important role in the evolution history of woolly rhinoceros. The fossils found in China last a long period, there are a large number of late Pleistocene fossils in northeastern China and Salawusu region, the sample source is very rich, and the temperature in these places is low all year round, all these are very conducive to the preservation of ancient DNA. Our samples were collected from the late Pleistocene stratigraphy, and the age of the samples does not exceed the theoretical retention period of ancient DNA, these provide very good research materials for our ancient DNA work. Up to now, ancient DNA studies to the woolly rhinoceros fossil materials collected from China are very limited though there are a lot of late Pleistocene fossils.
In this study, we obtained complete or partial cytochrome b sequences from eight late Pleistocene Coelodonta antiquitatis bones excavated from Salawusu (Inner Mongolia,42000YBP), Zhaodong (Heilongjiang Province,39000YBP) and Qinggang (Heilongjiang Province,35000YBP). The sequences obtained in this study enriched the GenBank data of woolly rhinoceros and they also make people better understand the genetic diversity of woolly rhinoceros samples, which were collected from different locations and belonged to different ages. At the molecular level, we reconstructed the phylogenetic trees of woolly rhinoceros, and this work improved us better understanding the phylogenetic status of Coelodonta antiquitatis from China. In addition, we also derived the divergence time between woolly rhinoceros and Sumatran rhinoceros using molecular clock. Firstly, we estimate the divergence time using the software MEGA4.0based on the split time between the equids and ceratomorpha (56Ma) or the split time between Artiodactyla and Cetacea (60Ma). We also carried out Bayesian analyse using the software of BEAST1.6.1and Markov chain Monte Carlo (MCMC) algorithm to estimate the divergence time based on the split time between the equids and ceratomorpha (56Ma). Secondly, we estimated the divergence time between woolly rhinoceros and Sumatran rhinoceros using the software Network4610based on the evolution rate of the cytochrome b gene as2%per million years. In addition, we tried to reveal the Eurasian migration of woolly rhinoceros.
We mainly drew the following conclusions:
(1) We obtained complete or partial cytochrome b gene sequences from eight woolly rhinoceros fossil materials collected from northeastern China and Salawusu region, the length of the sequences ranges from84bp to1140bp. Among them, we obtained the complete cytochrome b gene from the sample C.α._HS14, which was collected from Zhaodong, and to another Zhaodong sample C.α._HS12, we got the total length of1130bp cytochrome b gene fragment. To the Qinggang sample C. α._Qgl3, we got the length of490bp cytochrome b gene fragment. To the Salawusu sample C. α.SL1, we got the total length of651bp cytochrome b gene fragment, and to the other one Salawusu sample C. α._SL4, we got the total length of1100bp cytochrome b gene fragment. We have submitted the above gene sequences to GenBank respectively, and the GenBank accession numbers are GU371439(C.α._HS14), GU371440(C.α._HS12)、JQ974919(C.α._Qg13)、JQ974920(C.α.SL1) and JQ974921(C.α._SL4). The sequence length obtained from the other three samples is very short. To the sample C. a._Qg13collected from Qinggang, we only got84bp cytochrome b gene fragment. Another Qinggang sample C.α._Qg13, we only got140bp cytochrome b gene fragment. And to the sample C.α._SL5collected from Salawusu, we just got204bp cytochrome b gene fragment. The repeated experiments were carried out at the centre for ancient genetics, university of Copenhagen, and identical results were obtained, these all proved the sequences obtained in this study are true and reliable.
(2) In this study, we obtained ancient DNA sequences from late Pleistocene Coelodonta antiquitatis remains excavated from northeastern China and Salawusu region. Our studies revealed that the soil, climate and environment conditions of northern and northeastern China are suitable for the preservation of ancient DNA. But the preservation of our samples is not as good as the samples excavated from Belgium Scladina cave and Siberia permafrost. Moreover, the preservation of our samples is quite different even them from the same location and the same stratigraphy.
(3) Phylogenetic analyses show that all ancient Coelodonta antiquitatis samples analyzed are clustered together using both MEGA and Bayesian methods, this reveals that the sequences analyzed are homology. At the same time phylogenetic trees also show that Coelodonta antiquitatis group shared the closest relationship with the extant Sumatran rhinoceros. In addition, our results also reveal that the Coelodonta antiquitatis samples from Salawusu (C. α._SL1、C. α._SL4、C. α._SL5) together with one sample from Zhaodong County (C.α._HS14) appear at one sub-clade of the Coelodonta antiquitatis clade, the other samples from Zhaodong County and Qinggang County, Heilongjiang Province (C.α._HS12and C.α._Qg13) are grouped with the sample from Yakut, Russia (C.a._Willerslev). This may reflect the genetic exchange of woolly rhinoceros among the regions of northeastern China, Salawusu region and northern Asia during the late Pleistocene. Our study may reveal the migration of woolly rhinoceros, the typical periglacial animal. It dispersed from north to south or from south to north under the influence of climate change during the alternation of Quaternary glacial/interglacial periods.
(4) We calculated the divergence time between woolly rhinoceros and Sumatran rhinoceroses using two molecular clock methods. Firstly, based on the calibration standard of outgroup fossil records, we obtained woolly rhinoceros and Dicerorhinus sumatrensis diverged at about24.5-27.6Ma by using MEGA phylogenetic analyses and22.5Ma by using BEAST phylogenetic analyses. Secondly, we derived another estimate of the divergence time considering the evolution rate of the cytochrome b gene as2%per million years, the separation between woolly rhinoceros and Sumatran rhinoceros occurred at about3.8-4.7Ma. Compared the two different timescales derived from different molecular dating methods, We considered that the older timescale approach of using the fossil calibration of the outgroup may have overestimated the divergent event. We suggested that the younger timescale obtained by using the evolution rate of the cytochrome b gene as2%per million years is more likely, because this timescale is more consistent with the earliest known fossil record.
(5) We have analyzed the woolly rhinoceros cytochrome b sequences obtained in this study compared with previously published data from GenBank, the results indicated that woolly rhinoceros might be lack of genetic variation among analyzed samples in the late Pleistocene. Perhaps it is one of the important factor which led to woolly rhinoceros extinction at the beginning of Holocene. Considering the samples within differents regions, genetic diversity of woolly rhinoceros from Salawusu region is the highest, the genetic diversity of woolly rhinoceros from northeastern China is the second. Comparison sample gene diversity between regions, the results showed that gene diversity is the lowest between northeastern China samples and Yakut samples, and the gene diversity is relatively high between northeastern China samples and Salawusu samples.
1986年,随着聚合酶链式反应(PCR)技术的发明,特别是迅猛发展的分子生物学技术(多重PCR、大规模测序、高通量测序、直接多重测序、阵列序列捕获测序),使得从古代生物的遗体中提取并扩增DNA成为现实。古DNA作为遗传信息的载体,保存有生物遗传变异和生长发育的全部信息,为人们探寻漫长历史年代中生物种群系统发生与演变规律提供重要的研究资料,同时也为人们重建生物的起源与进化历程提供了一种新的研究方法。目前,古DNA技术在生物的起源、演化、迁移、遗传多样性等方面的研究中正发挥着越来越重要的作用。
从分子水平上,人们对披毛犀的古DNA研究工作开展的还非常有限。到目前为止,世界上公开报道的研究工作也非常少。Orlando等(2003)对采自比利时的披毛犀牙齿化石进行古DNA研究,他们利用所得到的完整12S rRNA和／或部分细胞色素b基因所构建的系统发育树显示,披毛犀与现生的苏门答腊犀牛亲缘关系最近。Binladen等(2006)对采自西伯利亚永久冻土中骨骼样品的线粒体DNA与核DNA基因的错配情况进行探讨。研究表明在线粒体DNA和核DNA中都存在着由于受损而遗传密码错配的情况,由胞嘧啶→胸腺嘧啶、鸟嘌呤→腺嘌呤的转换比胸腺嘧啶-→胞嘧啶、腺嘌呤→鸟嘌呤转换出现的次数多得多。这一研究结果显示,胞嘧啶的去氨基作用转变为尿嘧啶是古DNA(无论是线粒体DNA还是核DNA)错配的主要原因。Willerslev等(2009)从采自俄罗斯雅库特永久冻土中披毛犀的毛发中首次获取到披毛犀的完整线粒体基因。利用披毛犀和现生五种犀牛的线粒体基因构建的系统发育树显示,非洲的黑犀牛与白犀牛聚为一个分支,亚洲的爪哇犀牛与印度犀牛聚为一支；真披毛犀与苏门答腊犀牛聚为另一个分支。但是,根据构建系统发育树时所采用的基因不同或者选择不同的外类群,上述三个分支之间的关系就会发生变化。所以,披毛犀/苏门答腊犀牛、爪哇犀牛/印度犀牛、黑犀牛/白犀牛这三个分支之间的系统发育问题还未得到解决。
同时,Orlando等(2003)和Willerslev等(2009)还利用化石锚定点进行分子钟推算,得到披毛犀与苏门答腊犀牛的分歧时间为21-26Ma和17.5-22.8Ma,这与目前已知披毛犀的最早化石记录3.7Ma时间间隔差距较大。而且,Orlando等(2003)也指出他们关于披毛犀与苏门答腊犀牛分歧时间的计算是比较粗略的,因为基于同样化石标准进行分子钟估算,得到的结果与马属动物出现的时间不相符。所以,人们还需要做进一步的研究工作来探讨披毛犀与其近亲的分歧时间问题。
另外,Deng等(2011)为了评价西藏披毛犀(Coelodonta thibetana,3.7Ma)在犀亚科内的系统发育位置,利用17个犀牛属种：全部5种现生犀牛和12个绝灭的犀牛属种(包括已知的全部4种披毛犀：西藏披毛犀、泥河湾披毛犀、托洛戈伊披毛犀和真披毛犀)从形态学的角度进行了系统发育分析。研究结果表明苏门答腊犀牛既是两种现生独角犀牛(印度犀牛和爪哇犀牛)的姐妹群,也是披毛犀支系的姐妹群,或者两种独角犀(印度犀牛/爪哇犀牛)先与披毛犀支系形成姐妹群关系,而苏门答腊犀牛则是这个更大支系的姐妹群。而从分子水平上构建的系统发育树显示披毛犀与现生的苏门答腊犀牛亲缘关系最近。那么,这一形态学分析结论与来自分子水平的系统发育分析结果不一致。
披毛犀与现生的哪一种犀牛亲缘关系最近?披毛犀与其近亲的分歧时间?披毛犀在欧亚大陆之间的扩散时间?经历了何种扩散路线?披毛犀的绝灭等都是值得进一步研究的课题。
中国披毛犀在披毛犀的演化发展历史中占有非常重要的地位。我国发现的披毛犀化石,在地质时代上延续时间较长。在我国东北及萨拉乌苏地区保存有大量的晚更新世真披毛犀化石材料,样品来源丰富,而且这些地方气温常年偏低,也非常有利于古DNA的保存。本研究的样品采集于晚更新世地层中,不超出古DNA的理论保存年限10万年,这些都为披毛犀古DNA研究工作的顺利开展提供了很好的研究材料。到目前为止,在我国萨拉乌苏及东北地区存在有大量晚更新世披毛犀化石的情况下,对该地区晚更新世披毛犀化石材料的古DNA研究开展的还非常有限。
本研究利用采自我国内蒙古自治区的萨拉乌苏、黑龙江省的青冈和肇东地区晚更新世八个披毛犀骨骼样品材料(分别距今大约42000年、39000年和35000年),提取得到部分或完整披毛犀线粒体细胞色素b基因,不仅丰富了披毛犀的基因库,而且使人们了解我国不同地点、不同年代披毛犀的基因分异度。调集GenBank中披毛犀的同源序列以及现生犀牛序列,重建披毛犀的分子系统发育演化树,提高中国披毛犀系统演化分辨率。另外,本研究利用分子钟探讨了披毛犀与苏门答腊犀牛的分歧时间。首先利用外类群化石记录为锚定点,即马科动物和角型亚目的分歧时间(56Ma)、偶蹄目和鲸类的分歧时间(60Ma)为基准,利用MEGA4.0软件来推算披毛犀与现生的苏门答腊犀牛的分歧时间。基于化石记录马科动物和角型亚目的分歧时间56Ma,利用BEAST1.6.1软件贝叶斯马尔科夫链蒙特卡洛(MCMC)算法估算披毛犀与苏门答腊犀牛的分歧时间。其次,采用Network4610软件,基于细胞色素b基因的进化速率为2%/百万年来计算披毛犀与苏门答腊犀牛的分歧时间。此外,本研究还结合第四纪气候的变化,探讨披毛犀的欧亚迁移。
主要得到以下几点结论：
(1)从采自我国东北及萨拉乌苏地区八个披毛犀骨骼化石材料中,获取到84-1140bp长度不等的细胞色素b基因。其中肇东样品C.a._HS14得到完整细胞色素b基因,另一肇东样品C.a._HS12也得到长度为1130bp的细胞色素b基因片段,C. a._Qg13获得总共490bp的细胞色素b基因片段；C. a.SL1获得651bp的细胞色素b基因片段；C. a._SL4获得总长1100bp的细胞色素b基因片段。以上五个样品所获得的基因序列已提交GenBank, GenBank收录号分别为：GU371439、GU371440、JQ974919、JQ974920、 JQ974921。另外三个样品所获得的序列相对较短,青冈样品Cα._Qgll获得84bp的细胞色素b基因片段；青冈样品C. a._Qg14获得140bp的细胞色素b基因片段；萨拉乌苏样品C. a._SL5获得204bp的细胞色素b基因片段。重复性实验在哥本哈根大学的古DNA研究中心进行,证明本研究所得到的披毛犀序列是真实、可靠的。
(2)从我国东北及萨拉乌苏地区晚更新世披毛犀化石材料中提取到古DNA基因,说明我国萨拉乌苏及东北地区的土壤、气候环境条件比较适合于古DNA的保存。但从研究结果来看,这些样品的保存状况不及比利时洞穴和西伯利亚永冻土中真披毛犀样品保存的好,而且即使是同一地点、同一地层中的不同样品,保存状况也有较大差异。
(3)无论是用MEGA软件还是采用贝叶斯分析方法,所构建的分子系统发育树均显示所有的披毛犀样品都聚为一支,这反应其序列的同源性,且披毛犀与现生的苏门答腊犀牛亲缘关系最近。另外,从所构建的分子系统发育树还显示出,采自内蒙古自治区萨拉乌苏的样品(C. a._SL1、C. a._SL4、C. a._SL5)与一个黑龙江省肇东地区的样品(C a._HS14)聚为一个分支,采自黑龙江省肇东和青冈地区的其它样品(C. a._HS12、C. a._Qg13)与来自欧罗斯雅库特的样品(C. a_Willerslev)聚在一起,说明在晚更新世我国萨拉乌苏及东北地区的披毛犀与雅库特地区的披毛犀存在着基因交流,它反映了在第四纪冰期／间冰期的交替过程中,随着气候的变化,披毛犀这种典型的冰缘动物由北向南或由南向北的迁移。
(4)本研究采用两种分子钟方法来计算披毛犀与苏门答腊犀牛的分歧时间。首先,基于外类群中化石记录作为校正标准,利用MEGA软件系统发育分析推算出披毛犀与苏门答腊犀牛在24.5-27.6Ma产生分歧,利用BEAST软件进行系统发育分析推算出披毛犀与苏门答腊犀牛在22.5Ma产生分歧。其次,根据细胞色素b基因演化速率2%／百万年,利用Network软件推算出披毛犀与苏门答腊犀牛的分歧时间为3.8-4.7Ma。对于这两种分子钟方法推算出的两种分歧时间刻度,笔者认为利用外类群中已知化石的分歧时间来进行分子钟估算,得到的较老的分歧时间刻度高估了两者的分歧时间,而认为基于细胞色素b基因2%/百万年演化速率推算出的较近的分歧时间刻度较为可信,并且该分歧时间也与目前所知最早腔齿犀化石材料的年代相吻合。
(5)本研究中所获得不同地点、不同年代披毛犀的基因序列与GenBank中披毛犀序列相比较,发现在晚更新世披毛犀的遗传分异度比较低,或许遗传多样性的缺失是导致其绝灭的原因之一。比较不同地区披毛犀的基因分异度,结果显示我国萨拉乌苏地区披毛犀的遗传分异度最高,其次是我国东北地区。综合不同地区之间的情况来看,我国东北与雅库特和西伯利亚样品之间的基因分异度最低：我国东北与萨拉乌苏地区样品之间的基因分异度相对较高。
Woolly rhinoceros (Coelodonta antiquitatis Blummenbach,1799), an improvement species of Coelodonta(Coelodonta Bronn,1831), was highly adapted to the environment on cold grassland, periglacial tundra and permafrost tundra, which was gradually developed into a typical periglacial animal in the influence of Pleistocene glacial climate. During the Pleistocene, woolly rhinoceros was widely distributed in the Northern Hemisphere from72°N to33°N. The extensive woolly rhinoceros fossil records were found in northern Eurasia, but most of them belong to late Pleistocene. The early fossil records of the genus have been founded in several sites from China and the amount of early fossil materials is very limited. Up to now, the earliest representative of the genus, Coelodonta thibetana (3.7Ma), was found in the Zanda Basin in southwestern Tibet. Another early fossil record, Coelodonta nihowanensis (2.5Ma), was found in the Linxia Basin in Gansu Province, China. Comparably, the earliest fossil species outside China appeared later than that from China. A typical representative, Coelodonta tologoijensis (0.75Ma), has been found around the early middle Pleistocene in Buryatia, Russian Federation. In Europe, Coelodonta first appeared around400-460ka according to several early fossil records (such as Romania). Therefore, some researchers suggested that the woolly rhinoceros (Coelodonta) may have originated in China. After the origination of this genus in Asia, it diffused to eastern and central Europe in the middle Pleistocene for the first time, and gradually evolved to adapt the life on the cold tundra and steppe in the influence of Quaternary glacial climate, and it finally evolved into the most famous ice age animal——the true woolly rhinoceros (Coelodonta antiquitatis). After the origination of this species in Europe, it dispersed to north Asia and China in the following cold and dry period. Due to the incompleteness of the fossil record, especially the lack of early fossil records and very limited sampling sites, our understanding on its origin, migration, evolution and other issues is very ambiguous.
In1986, with the invention of polymerase chain reaction (PCR) technology, especially the rapid development of molecular biology technology (multiple PCR, large scale sequencing, high throughput sequencing, direct multiplex sequencing, array-based sequence and so on), the extraction and amplification of DNA from ancient biological remains come true. Ancient DNA, as the carrier of genetic information, contains all the information of biological genetic variation and growth. It could provide important research data for people to explore the occurrence of biological system and evolution during the long history. At the same time, it also provides us a new research method to rebuild the origin and evolution process of life. So ancient DNA technology is playing more and more important role in the the study of origin, evolution, migration and genetic diversity of life.
At the molecular level, the study on woolly rhinoceros is very limited. Until now, there are only several cases reported in the world. Orlando et al.(2003) extracted complete12S rRNA gene and partial cytochrome b gene of woolly rhinocers collected from Belgium. Based on the sequences, they performed the phylogenetic analyses and the results indicated that woolly rhinoceros is more closely related to extant Dicerorhinus sumatrensis. Binladen et al.(2006) investigated the frequency and types of miscoding lesions in mtDNA and nuDNA marks using two woolly rhinoceros permafrost bone samples, suggesting that there was no significant evidence for nuDNA sequences being more prone to miscoding lesions than mtDNA sequences, the conversion ratio from cytosine into thymine and from guanine into adenine occured more rates than that from Thymine into cytosine and from adenine into guanine. This study indicated that the deamination from cytosine into uracil is the main mismatch in ancient DNA ((both mitochondrial DNA and nuclear DNA). Willerslev et al.(2009) first obtained the whole mitochondrial genome sequences of woolly rhinoceros collected from permafrost inYakutia, Russian. Using the obtained mitochondrial DNA of woolly rhinoceros together with five extant rhino mitochondrial genome sequences, phylogenetic analysis was performed and the results indicated that the six species clustered into three sister groups:Diceros bicornis ICeratotherium simum, Rhinoceros sondaicus/Rhinoceros unicornis, Coelodonta antiquitatis I Dicerorhinus sumatrensis. However, the rhinoceros phylogenetic trees are highly diffuse, the relationship between the three branches will change when using different genes or different out groups. So, the phylogenetic issue between Coelodonta antiquitatis/Dicerorhinus sumatrensis, Rhinoceros sondaicus/Rhinoceros unicornis, Diceros bicornis ICeratotherium simum has not been resolved.
Orlando et al.(2003) and Willerslev et al.(2009) carried out the molecular clock calculations based on the calibration time points of out groups, and they obstained the divergent timescales21-26Ma and17.5-22.8Ma for woolly rhinoceros from Sumatran rhinoceros, there is a big gap between these timescales and the known earlist fossil record of woolly rhinoceros. Moreover, Orlando et al.(2003) also pointed out the evolutionary timescale for woolly rhinoceros from Sumatran rhinoceros should be taken as preliminary because the same calibration failed to recover the date of emergence of the Equus genus. So, people need to do further researches to explore the divergence time between woolly rhinoceros and its relatives.
In addition, to investigate phylogenetic status of Coelodonta thibetana (3.7Ma), Deng et al.(2011) reconstructed phylogenetic trees based on the morphological data, using seventeen rhinoceros genera which contained all the five extant rhinoceros and twelve extinct rhinoceros (including all the known extinct Coelodonta:Coelodonta thibetana, Coelodonta nihowanensis, Coelodonta tologoijensis and Coelodonta antiquitatis). The results show that Dicerorhinus sumatrensis clustered together with two extant one-horned rhinoceros (Rhinoceros sondaicus/Rhinoceros unicornis) to form a sister group, it also formed a sister group with the branch of Coelodonta, or two extant one-horned rhinoceros first clustered together with the branch of Coelodonta, and then Dicerorhinus sumatrensis formed a sister group with the larger branch. However, at the molecular level, the the phylogenetic trees showed that woolly rhinoceros is most closely related to one of the extant rhinoceros species, Sumatran rhinoceros, and this result was inconsistent with the study based on morphological data.
Which extant rhinoceros is more closely related to woolly rhinoceros? When did woolly rhinoceros separate from its relatives? When did Coelodonta diffuse from Asia to Europe? What routes did it experience during the process of migration? And other issues such as its extinction also need further exploration.
Woolly rhinoceros remains from China occupy a very important role in the evolution history of woolly rhinoceros. The fossils found in China last a long period, there are a large number of late Pleistocene fossils in northeastern China and Salawusu region, the sample source is very rich, and the temperature in these places is low all year round, all these are very conducive to the preservation of ancient DNA. Our samples were collected from the late Pleistocene stratigraphy, and the age of the samples does not exceed the theoretical retention period of ancient DNA, these provide very good research materials for our ancient DNA work. Up to now, ancient DNA studies to the woolly rhinoceros fossil materials collected from China are very limited though there are a lot of late Pleistocene fossils.
In this study, we obtained complete or partial cytochrome b sequences from eight late Pleistocene Coelodonta antiquitatis bones excavated from Salawusu (Inner Mongolia,42000YBP), Zhaodong (Heilongjiang Province,39000YBP) and Qinggang (Heilongjiang Province,35000YBP). The sequences obtained in this study enriched the GenBank data of woolly rhinoceros and they also make people better understand the genetic diversity of woolly rhinoceros samples, which were collected from different locations and belonged to different ages. At the molecular level, we reconstructed the phylogenetic trees of woolly rhinoceros, and this work improved us better understanding the phylogenetic status of Coelodonta antiquitatis from China. In addition, we also derived the divergence time between woolly rhinoceros and Sumatran rhinoceros using molecular clock. Firstly, we estimate the divergence time using the software MEGA4.0based on the split time between the equids and ceratomorpha (56Ma) or the split time between Artiodactyla and Cetacea (60Ma). We also carried out Bayesian analyse using the software of BEAST1.6.1and Markov chain Monte Carlo (MCMC) algorithm to estimate the divergence time based on the split time between the equids and ceratomorpha (56Ma). Secondly, we estimated the divergence time between woolly rhinoceros and Sumatran rhinoceros using the software Network4610based on the evolution rate of the cytochrome b gene as2%per million years. In addition, we tried to reveal the Eurasian migration of woolly rhinoceros.
We mainly drew the following conclusions:
(1) We obtained complete or partial cytochrome b gene sequences from eight woolly rhinoceros fossil materials collected from northeastern China and Salawusu region, the length of the sequences ranges from84bp to1140bp. Among them, we obtained the complete cytochrome b gene from the sample C.α._HS14, which was collected from Zhaodong, and to another Zhaodong sample C.α._HS12, we got the total length of1130bp cytochrome b gene fragment. To the Qinggang sample C. α._Qgl3, we got the length of490bp cytochrome b gene fragment. To the Salawusu sample C. α.SL1, we got the total length of651bp cytochrome b gene fragment, and to the other one Salawusu sample C. α._SL4, we got the total length of1100bp cytochrome b gene fragment. We have submitted the above gene sequences to GenBank respectively, and the GenBank accession numbers are GU371439(C.α._HS14), GU371440(C.α._HS12)、JQ974919(C.α._Qg13)、JQ974920(C.α.SL1) and JQ974921(C.α._SL4). The sequence length obtained from the other three samples is very short. To the sample C. a._Qg13collected from Qinggang, we only got84bp cytochrome b gene fragment. Another Qinggang sample C.α._Qg13, we only got140bp cytochrome b gene fragment. And to the sample C.α._SL5collected from Salawusu, we just got204bp cytochrome b gene fragment. The repeated experiments were carried out at the centre for ancient genetics, university of Copenhagen, and identical results were obtained, these all proved the sequences obtained in this study are true and reliable.
(2) In this study, we obtained ancient DNA sequences from late Pleistocene Coelodonta antiquitatis remains excavated from northeastern China and Salawusu region. Our studies revealed that the soil, climate and environment conditions of northern and northeastern China are suitable for the preservation of ancient DNA. But the preservation of our samples is not as good as the samples excavated from Belgium Scladina cave and Siberia permafrost. Moreover, the preservation of our samples is quite different even them from the same location and the same stratigraphy.
(3) Phylogenetic analyses show that all ancient Coelodonta antiquitatis samples analyzed are clustered together using both MEGA and Bayesian methods, this reveals that the sequences analyzed are homology. At the same time phylogenetic trees also show that Coelodonta antiquitatis group shared the closest relationship with the extant Sumatran rhinoceros. In addition, our results also reveal that the Coelodonta antiquitatis samples from Salawusu (C. α._SL1、C. α._SL4、C. α._SL5) together with one sample from Zhaodong County (C.α._HS14) appear at one sub-clade of the Coelodonta antiquitatis clade, the other samples from Zhaodong County and Qinggang County, Heilongjiang Province (C.α._HS12and C.α._Qg13) are grouped with the sample from Yakut, Russia (C.a._Willerslev). This may reflect the genetic exchange of woolly rhinoceros among the regions of northeastern China, Salawusu region and northern Asia during the late Pleistocene. Our study may reveal the migration of woolly rhinoceros, the typical periglacial animal. It dispersed from north to south or from south to north under the influence of climate change during the alternation of Quaternary glacial/interglacial periods.
(4) We calculated the divergence time between woolly rhinoceros and Sumatran rhinoceroses using two molecular clock methods. Firstly, based on the calibration standard of outgroup fossil records, we obtained woolly rhinoceros and Dicerorhinus sumatrensis diverged at about24.5-27.6Ma by using MEGA phylogenetic analyses and22.5Ma by using BEAST phylogenetic analyses. Secondly, we derived another estimate of the divergence time considering the evolution rate of the cytochrome b gene as2%per million years, the separation between woolly rhinoceros and Sumatran rhinoceros occurred at about3.8-4.7Ma. Compared the two different timescales derived from different molecular dating methods, We considered that the older timescale approach of using the fossil calibration of the outgroup may have overestimated the divergent event. We suggested that the younger timescale obtained by using the evolution rate of the cytochrome b gene as2%per million years is more likely, because this timescale is more consistent with the earliest known fossil record.
(5) We have analyzed the woolly rhinoceros cytochrome b sequences obtained in this study compared with previously published data from GenBank, the results indicated that woolly rhinoceros might be lack of genetic variation among analyzed samples in the late Pleistocene. Perhaps it is one of the important factor which led to woolly rhinoceros extinction at the beginning of Holocene. Considering the samples within differents regions, genetic diversity of woolly rhinoceros from Salawusu region is the highest, the genetic diversity of woolly rhinoceros from northeastern China is the second. Comparison sample gene diversity between regions, the results showed that gene diversity is the lowest between northeastern China samples and Yakut samples, and the gene diversity is relatively high between northeastern China samples and Salawusu samples.
引文
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