外文翻译--Origins of the Chinese yak evidence from maternal and paternal inheritance

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1、Origins of the Chinese yak: evidence from maternal and paternal inheritance Yuliang Xie1, Yinxia Li1, Xingbo Zhao2, Xiang Zhang1, Ning Li2, Zhuang Xie1, Honglin Liu1, Qifa Li1 1 College of Animal Science and Technology Nanjing Agricultural University Nanjing 210095, P.R. China 2 State Key Laboratory

2、 for Agribiotechnology China Agricultural University Beijing 100094, P.R. China e-mail: AbstractIt is well understood that the yak originates from China, but facts regarding origin time and evolutionary relationship with other species of Bovini, are largely disputed. Here, we have analyzed the phyl

3、ogenetic relationship of eight representative species of Bovini, based on the Cytochrome b gene of mitochondrial DNA and TSPY gene of chromosome Y. We also estimated the divergence times of these different species. Results showed that the divergence time of domestic yak (Poephagus grunniens) and wil

4、d yak (Poephagus mutus) was 0.28 MYA. Considering archaeology evidence and historical records, we suggest that the domestic yak and todays wild yak shared one common ancestor, the primitive yak, 0.28 MYA. For the yak and American bison, the sequence divergence is the lowest (3.80, 0.50) and the dive

5、rgence time is the latest (0.85 - 1.19 MYA), less than that between yak and cattle/zebu (8.30, 0.75 and 1.70 - 2.15 MYA). Phylogenetic analysis indicates that the yak and American bison were clustered together. Investigation of maternal inheritance (Cytochrome b) and paternal inheritance (TSPY) also

6、 proved that the genetic relationship between the yak and American bison was the closest, they evolved from one common ancestor, and their divergence time was later, during the metaphase of Pleistocene. Keywords-Chinese yak; Bovini; Cytochrome b gene; TSPY gene; origin; phylogenetic relationship 1 I

7、NTRODUCTION The yak is the only species of Bovini which can thrive and reproduce in the Qinghai-Tibet Plateau which is known for its high elevation of more than 3500m, chilly weather, oxygen shortage, large temperature difference between day and night, and strong ultraviolet radiation. Despite its e

8、nvironment, the yak has adapted rigorously over thousands of years through natural and artificial selection and has a great anti-adversity capacity. The yak is an important production animal for people of this area, who refer to the species reverently as the “boat of Plateau” and “all-powerful lives

9、tock” (Wiener et al., 2003; Li et al., 2004). China currently has the largest yak population with approximately 95% of the worlds total yak, with the other 5% scattered throughout Mongolia, Russia, Nepal, India, Bhutan, Sikkim and Pakistan (Gu et al., 2007). The yak (domestic and wild yak), originat

10、ed from China, and is considered an ancient species. Based on petrifactions found in Northern China, Inner Mongolia, Siberia, and Alaska, researchers suggest that the forefather of the domestic yak (Poephagus grunniens) and todays wild yak (Poephagus mutus) was a primitive wild yak that lived about

11、2.50 million years ago (MYA) (Hou, 1991; Cai, 1992). Investigation of 20 microsatellite loci indicates that the divergence time between yak and cattle (Bos taurus) was 0.571.53 MYA, between yak and the American bison (Bison bison) was 0.391.04 MYA (Ritz et al., 2001). Some researchers, using 2065bp

12、nucleotide sequences (including 2 mitochondrial gene sequences and lactoferrin promoter sequences) of Bovini, found that the yak has the closest genetic relationship with the American bison. They estimated that the divergence time between them was 1.392.21 MYA (Hassanin and Ropiquet, 2004) using 206

13、5bp nucleotide sequences. At this point in time, information regarding the origin of the yak is inconsistent and researchers are unable to reach a consensus. During the Paleolithic era (500010000 years ago), the ancient Qiang people of China (ancestors of the modern-day Tibetan peoples) that populat

14、ed the Qiangtang area of northern Tibet, captured and domesticated wild yak for agricultural use (Olsen, 1990; Wiener et al., 2003; Li et al., 2006). During the1950s, in the Linzhi and Changdu areas of Tibet, the Chaidamu area of Qinghai, and the Kangding area of Sichuan, Chinese archaeologists disc

15、overed petrifactions indicating that the domestic yak appeared 4500 years ago. This conclusion was consistent with discoveries by Li et al. (2004) who used microsatellite markers to determine the period of origin. The yak has similar morphological characteristics to cattle and American bison, so res

16、earchers focused on the phylogenetic relationship between yak and other species of Bovini (Li et al., 2006; Gu et al., 2007). Groves (1981) looked at the skull features of different species of Bovini and concluded that the yak had a closer phylogenetic relationship with American bison than with catt

17、le. This conclusion was consistent with Geraads (1992), Li et al. (2005), and Hassanin and Ropiquet (2004), who studied characteristics of the skeleton, DRB3 gene sequences, and mitochondrial DNA and lactoferrin gene sequences, respectively. Conversely, 978-1-4244-4713-8/10/$25.00 2010 IEEEaccording

18、 to the different morphological characteristics of each species, Bohlken (1958, 1961) established a phylogenetic tree for Bovini and concluded that the genetic relationship between the yak and cattle was closer than between the yak and American bison, consistent with Hartl et al. (1988) and Ritz et

19、al. (2001) who looked at blood and microsatellite loci, respectively. To study origins of the yak and the phylogenetic relationship between the yak and other species of Bovini, we investigated the complete Cytochrome b gene sequences of yak and partial TSPY gene sequences of chromosome Y. We also co

20、mpared the differences between the sequences of yak and that of other species of Bovini (Bos taurus, Bos indicus, Bison bison, Bison bonasus, Bubalus bubalis and Sycenrus caffer) and analyzed the phylogenetic relationship. The origin of the yak and its phylogenetic relationship with other species of

21、 Bovini are discussed from the perspective of paternal and maternal inheritance. 2 MATERIALS AND METHODS 2.1 Samples Blood samples from one male and one female domestic yak (Poephagus grunniens) were collected at the Longri Sire Nursery (Sichuan Province, China). Genomic DNA was extracted using stan

22、dard phenol/chloroform methods. The representative species of Bovini included Poephagus grunniens, Poephagus mutus, Bos indicus, Bison bison, Bison bonasus, Bubalus bubalis and Sycenrus caffer. We also collected samples from sheep (Ovis aries), because of its close phylogenetic relationship with Bov

23、ini, as the outgroup for phylogenetic analysis. We obtained Cytochrome b and TSPY gene sequences of the above-mentioned species searching the GenBank database and literature tracking (Table 1). TABLE 1 LIST OF TAXONOMIC SAMPLES AND GENBANK ACCESSION NUMBERS Species GenBank Accession No. Cytochrome b

24、 TSPY Poephagus grunniens AY374124* EU881363* Poephagus mutus AY955226 Bos taurus AY526085 AY347587 Bos indicus AF492350 AY347588 Bison bison AF036273 AY347591 Bison bonasus Y15005 AY347592 Bubalus bubalis D88631 EF180050 Sycenrus caffer D82888 Ovis aries AF010406 U30305 * Sequences produced from ou

25、r research 2.2 PCR, cloning and sequencing PCR primers were designed based on the mitochondrial genome sequence (GenBank Accession No. AY526085) and TSPY gene sequence (GenBank Accession No. NW_001506530) of cattle (Bos taurus). The primer sequences of Cytochrome b were Ucytb, 5-CCA TAA ATAG GTG AAG

26、 GTT TCG-3, and Dcytb, 5-TTG ATG GTG AGA CTG CAG TT-3. The primer sequences of TSPY were Utspy, 5-TTC TGG GAC TTT GAA CGG G-3, and Dtspy, 5-TGT TTT GGA TTT GGT CTA A-3. Each 25L PCR reaction contained 30ng of genomic DNA, 1.5mmol/L MgCl2, 2.5mL 10 reaction buffer, 0.2mmol/L of dNTP, 1.0U of Taq DNA

27、polymerase, and 0.2mol/L of each primer. Amplification consisted of initial denaturalization at 94C for 5 min and 35 amplification cycles including denaturalization at 94C for 30 s, annealing at 64C (54C for TSPY) for 45 s, extension at 72C for 1 min, and a final extension at 72C for 10 min. The pur

28、ified PCR products were obtained using a Geneclean III Kit (Q. Biogene, Carlsbad, CA, USA) were ligated to the pMD 18-T vector (TaKaRa, Dalian, China) according to the manufacturers instructions, and then transformed into competent DH5 cells. The plasmid DNA was extracted using a BioDev Plasmid Rapi

29、d Isolation Kit (BioDev, Beijing, China) and sequenced on a Model ABI377 Fluorescent Sequencer (ABI, Foster, CA, USA). 2.3 Statistical and phylogenetic analysis The analyses of sequence alignment, arrangement and the sequence divergence were carried out using DNAStars5.02 software (DNASTAR Inc., 199

30、6). The transition/transversion (Ts/Tv) was accounted for using MEGA4.1 software (Tamura et al, 2007). Phylogenetic trees of Bovini were constructed using the maximum parsimony method of MEGA4.1 software (Tamura et al, 2007) by selecting the Kimura 2-parameter model. Bootstrap percentage values were

31、 obtained by bootstrap replications test (1000 replications). According to the formula T = K/2r (Li 1997), the divergence time of different species of Bovini was estimated. In this formula, T, K, and r stand for divergence time, sequence divergence and substitution rate, respectively. 3 RESULTS 3.1

32、Phylogenetic tree of Bovini based on mitochondrial Cytochrome b gene sequences Based on 1140bp mitochondrial Cytochrome b gene sequences, a phylogenetic tree of Bovini was constructed using the Maximum parsimony method (Fig. 1). Figure 1 shows that Bovini were clustered in one group, while the outgr

33、oup (sheep, Ovis aries) was clustered in another group. Bovini, which had eight species, could be divided into two groups. Buffalo, including Bubalus bubalis (Asian buffalo) and Sycenrus caffer (African buffalo), were clustered in one group (BP = 89%), with the other six species clustered in one gro

34、up (BP = 100%). Among the six species of Bovini, Poephagus grunniens (domestic yak) and Poephagus mutus (wild yak) were initially clustered in one group (BP = 99%), then clustered with Bison bison (American bison) in one group (BP = 94%). Meanwhile, Bos taurus (cattle) was firstly clustered with Bos

35、 indicus (zebu) (BP = 100%), then clustered with Bison bonasus (European bison) (BP = 93%). Figure1. Phylogenetic tree of Bovini based on Cytochrome b gene sequences by Maximum parsimony method. The nodal parameters support the 1000 times repetition analysis on sampling examination. 3.2 Phylogenetic

36、 tree of Bovini based on Y chromosome TSPY gene sequences Based on 933bp Y chromosome TSPY gene sequences, a phylogenetic tree of Bovini was constructed using the MP method (Fig. 2). Figure 2 shows that Bovini were clustered in one group, while the outgroup (sheep, Ovis aries) was clustered in anoth

37、er group. Among Bovini, Poephagus grunniens (domestic yak), Bison bison (American bison) and Bison bonasus (European bison) were clustered in one group (BP = 58%), Bos taurus (cattle) was clustered with Bos indicus (zebu) in one group (BP = 99%), while Bubalus bubalis (Asian buffalo) was clustered a

38、lone. Figure2 Phylogenetic tree of Bovini based on TSPY gene sequences by Maximum parsimony method. The nodal parameters support the 1000 times repetition analysis on sampling examination. 3.3 Estimation of divergence time of different species of Bovini The transition/transversion (Ts/Tv) rate of Cy

39、tochrome b among the different species of Bovini was 5.5, higher than the critical value 2.0 (Knight and Mindell, 1993) and showed higher transition bias. Therefore, the molecular clock of the Cytochrome b gene sequence was 2% per million years in Bovinae, which was consistent with Birungi and Arcta

40、nder (2001), and was chosen to estimate the divergence time of different species of Bovini. The sequence divergence of Cytochrome b between domestic yak and wild yak was 1.1 and the divergence time was 0.28 MYA. The sequence divergences of Cytochrome b among yak (domestic yak and wild yak), cattle/z

41、ebu, and American bison were 8.08.6 and 3.44.2, respectively. Divergence times were 2.002.15 MYA, and 0.851.05 MYA, respectively. We can see that the divergence time between the yak and American bison was later, compared with other Bovini species. The divergence times (sequence divergence) between t

42、he yak and European bison, Asian buffalo, African buffalo were 1.952.05 MYA (7.88.2), 3.383.43 MYA (13.513.7), and 3.253.38 MYA (13.0-13.5), respectively. According to human TSPY gene 2.15 0.06 10-9/site/year mutation rate (Bhowmick et al., 2006), we estimated the divergence time among different spe

43、cies of Bovini. The sequence divergence of TSPY between the yak and cattle/zebu was 0.75, and we predicted that the divergence time was 1.701.80 MYA. The sequence divergence of TSPY between the yak and American bison was 0.5, and we predict that the divergence time was 1.131.19 MYA. We can see that

44、the divergence time between the yak and American bison was later, which was consistent with studies using mitochondrial Cytochrome b gene. The sequence divergence of TSPY between cattle/zebu, and American bison, the yak and Asian buffalo were 0.65 and 8.10, and the divergence times were 1.471.56 MYA

45、 and 18.4019.38 MYA, respectively. 4. DISCUSSION 4.1 Origin of the Chinese yak The yak originates from China (Cai, 1992), and the origins of the Chinese yak has been a major focus for researchers (Li et al., 2006; Guo et al., 2006; Gu et al., 2007; Li et al., 2008). The primary source of origin info

46、rmation has been Pleistocene wild yak fossils found in northern China, Inner Mongolia, eastern Siberia, Alaska and north of Central Asia. It is obvious now that the yak has been existence in northeast Eurasia from the new tertiary period, 2.5 million years ago. The original yak of the new tertiary p

47、eriod was probably a close ancestor of the domestic yak and todays yak. However, during the Quaternary Ice Age, the original yak was affected by changes in climate and migrated southward into the central Tibetan plateau, which became the distributing area of todays yak. The yak of northeast Eurasia

48、did not migrate and died out (Hou, 1991; Cai, 1992). The domestic yak was domesticated from wild yak (Qiu et al., 1986; Olsen et al., 1990). During the Paleolithic era, about 500010000 years ago, the ancient Qiang people in the Qiangtang area of northern Tibet, had domesticated wild yak over a long

49、period of time. Evidence has been found that the yak breeding industry emerged during the Longshan cultural period during the terminal Neolithic era (about 2,800BC2,300BC) (Qian, 1979; Cai, 1992). Chinese archaeologists have found domestic yak fossils and related cultural relics dated about 4500 yea

50、rs ago from Linzhi and Changdu in Tibet, Chaidamu in Qinghai, and Kangding in Sichuan (Liu et al., 1989). The fossils show that the yak was domesticated 4500 years ago. According to investigations of 20 microsatellite loci, Li et al. (2004) estimated that the divergence time of Chinese yak was 8000

51、years ago, which is consistent with historical data and archaeological research. Based on the complete sequences of Cytochrome b, we suggest that the divergence time of domestic yak and wild yak was about 0.28 MYA, earlier than archaeology findings (about 4500 years ago), the historical recorded tim

52、e of yak domestication (500010000 years ago) and the earliest divergence time of Chinese yak presumed by 20 microsatellite loci (8000 years ago). This shows that the yak was not domesticated from todays wild yak directly, but evolved from wild yak 0.28 MYA and domesticated by the ancient Qiang peopl

53、e. The wild yak lived 0.28 MYA and was probably a close evolutionary ancestor of the domestic yak and todays wild yak. The divergence times of the yak and American bison were about 0.851.05 MYA (Cytochrome b gene sequence) and 1.131.19 MYA (TSPY gene sequence), which is consistent with that presumed

54、 by mtDNA-RFLP (1.102.20 MYA) (Tu et al., 2002) but earlier than that presumed by microsatellite loci (0.571.53 MYA) (Ritz et al., 2000). The divergence time between zebu and cattle was 0.4 MYA, which is consistent with studies using microsatellite loci (0.310.82 MYA) (Ritz et al., 2000) and mtDNA R

55、FLP (0.30.5MYA) (Kikkawa et al., 1995). The divergence time between yak and cattle/zebu was far earlier than that of cattle and zebu, yak and American bison. We thought it was not possible that the ancestor of the yak was divergent from a close ancestor of cattle and zebu, but probably from an ances

56、tor of American bison. That is to say, the yak and American bison probably have a common direct ancestor. Based on this study and fossil records (Flerow, 1980; Hou, 1991; Cai, 1992), historical data (Qian, 1979; Cai, 1992), archaeological discoveries (Liu et al., 1989) and molecular biology data (Ha

57、ssanin and Ropiquet, 2004; Guo et al., 2006; Li et al., 2008), we have estimated the approximate evolutionary history of the yak. During the Quaternary period, in north-east Eurasia, the original wild yak and American bison differentiated due to climate changes. When the ice age was over and this ar

58、ea became warmer, the yak moved south to the colder climates of the Qinghai-Tibetan Plateau, and differentiated during the metaphase of the Pleistocene era. Some ancient yaks evolved into todays wild yak, others were domesticated by the ancestor Qiang people 4500 years ago. 4.2 The phylogenetic rela

59、tionship between yak and other species of Bovini The yak looks like a common, beefy, small bodied cattle. It is closely related to other species of Bovini (e.g. Bos taurus, Bison bison). The molecular evolution and phylogenesis of Bovini is therefore of great interest. During the 1990s, the phylogen

60、etic relationship among the species of Bovini was studied by mainly investigating morphological characteristics, bone characteristics, fossils, and blood protein polymorphism. Two outcomes were determined: one was that the genetic relationship between yak and cattle/zebu was close and clustered in o

61、ne group (Bohlken, 1961; Hartl et al., 1988); the other was that the genetic relationship between the yak and American bison was also close and clustered in one group (Groves, 1981; Olsen, 1990; Geraads, 1992). Ritz et al. (2000) found that the genetic relationship between yak, cattle and zebu was c

62、lose by studying 20 microsatellite loci. Buntjer et al. (2002) found the genetic relationship between yak and American bison was close though the study of the AFLP marker, which was consistent with the study of DRB3 gene sequences by Li et al. (2005). At present, the study on the phylogenetic relati

63、onship among the species of Bovini mainly uses mitochondrial DNA sequence, and the results are basically consistent. The genetic relationship between yak and American bison is close, the genetic relationship between cattle/zebu and European bison is closer, while, the genetic relationship between ya

64、k and cattle/zebu is farther (Kraus et al., 1992; Janecek et al., 1996; Ward et al., 1999; Hassanin and Douzery, 1999; Verkaar et al., 2004; Guo et al., 2006; Hassanin and Ropiquet, 2004, 2007; Li et al., 2008). Based on the 1140bp mitochondrial Cytochrome b complete sequence and 933bp Y chromosome

65、TSPY partial sequence, we found that the sequence divergence of Cytochrome b and TSPY genes between the yak and American bison were 3.80 and 0.50 respectively, which were less than that between yak and cattle/zebu (8.30, 0.75). Phylogenetic analysis found that yak were clustered with American bison,

66、 but not clustered with cattle/zebu. According to the 2% per million years mutation rate of Cytochrome b and the mutation rate of TSPY 2.15 0.06 109/site/year, we speculated that the divergence times between yak and American bison were close, which were 0.851.05 MYA and 1.131.19MYA respectively, cle

67、arly less than that between other species of Bovini. The results of maternal genetic (mitochondrial Cytochrome b) and paternal genetic (Y chromosome TSPY) analyses were basically consistent:in Bovini, the yak has the closest genetic relationship with American bison, and the divergence time between t

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