Christopher U Orji1*, Ignatius O Onyeocha2, Steven S Shaida3, Peter M Dede4, Bitrus Yakubu5, Elijah E Ella6 and Pam D Luka5
...ochrome b (CytB), twelve haplotypes were generated for G. p. palpalis and five for G. m. submorsitans. Similarly, for the combined loci, haplotype diversity (Hd) was higher for G. p. palpalis (0.90) than G. m. submorsitans (0.68). Nucleotide diversity was homogenous for G. m. submorsitans (0.24859) than G. p. palpalis (0.24093). A higher genetic diversity suggests a higher evolutionary rate. Haplotype diversity and Nuc...
Pan-pan Guo1, Wei Liu2, Yan Li2, Rui-yu Ma2, Wang Zaigui1*, Kai Zhan2*, Jun-ying Li2 and Sheng-nan Liu2
.... Additionally, four HTT haplotypes (H1: GG; H2: GC; H3: AG; H4: AC) and their frequency distributions were estimated using the phase program. Haplotypes combinations constructed on these two SNPs of HTT gene were associated with some reproduction traits. In particular, diplotype H1H1 had positive effect on reproduction traits, diplotype H2H4 had negative effect of reproduction traits. In conclusion, our study showed that po...
Lingtong Ye1, Chao Cao1,2, Bin Tang1,2, Tuo Yao1, Ruixuan Wang1 and Jiangyong Wang1*
...me larvae share the same haplotypes as adults. These findings clearly indicate that the larvae collected from sea waters around an oyster farm belong to P. websteri, the same species as the adult worms collected from the oyster Crassostrea hongkongensis in that locality. Two polydorid-specific primers were successfully designed, for the first time, to amplify target fragments of the COI gene. This study is the first to molecularly validate uniden...
Jun Gao1,2, Liang-Liang Yue3, Xianhuan Jiang1, Liju Ni4, Muhammad Aqeel Ashraf5, Yuxun Zhou,1 Kai Li1,* and Junhua Xiao1,*
...R) were sequenced and 49 haplotypes were observed. No shared haplotype was found among different geographic populations. High Fst values among the populations suggested that fragmentation of habitat has resulted in genetically distinct populations. The trees, inferred from maximum likelihood and Bayesian phylogenetic analysis, highly supported all the M. fortis individuals clustering into one monophyletic lineage. Three main clades are...
Wang-Dui Basang1, Tian-Wu An2, Luo-Bu Danjiu3, Yan-Bin Zhu1, Shi-Cheng He3, Xiao-Lin Luo2, Wei-Wei Ni4, Xiao Wang4, Shu-Zhu Cheng4, Jian Wang4 and Guang-Xin E4,*
... number variants, and 59 haplotypes were detected. The number of haplotypes within the population ranged from 17 (SN and JL) to 28 (DX). The haplotype diversity ranged from 0.9420 (SN) to 0.9770 (NR). The highest nucleotide diversity was found in the JL population (0.01479), whereas the lowest was found in the SN (0.00894) population. Phylogenetic analysis revealed that these four populations separated into two haplogroups; ...
Yuan Li1, Liyan Zhang2, Karhoe Loh3, Ji Feng1, Xinqing Zheng1, Puqing Song1 and Longshan Lin1,*
... the distribution of the haplotypes, an ancestral haplotype existed in both the Chinese population and the Malaysian population, further confirming that the Chinese and Malaysian P. minor populations originated from the same refuge in the South China Sea. A historical demographic analysis indicated that P. minor experienced a recent population expansion during the late Pleistocene period. Due to the need of P. minor to adapt to the diverse...
Fehmeeda Fatima, Asif Nadeem* and Maryam Javed
...ted. The total number of haplotypes (h) was found to be 17 and haplotype diversity (Hd) was 0.862. Nucleotide diversity (pi) was calculated to be 0.00210 and Tajima’s D neutrality test for neutral mutation indicated a negative value. Moreover, the results of homology analysis showed maximum similarity with sequences of goat and sheep sequences (partial) and were found to be 99.93% and 99.35%, respectively which was further confirmed by constructin...
Aiguo Zhou1,3,4, Shaolin Xie1,4, Zhenlu Wang1, Lanfen Fan1, Yanfeng Chen2, QiaoYe1, Fang Zeng1 and Jixing Zou1,*
... 0.000 to 0.002. For the haplotypes of two color morphs of Channa argus, the mean pair-wise genetic distances were estimated as 0.002, which were within the intra-species genetic distance interval for Channa species, indicating that they belonged to the same species, but not subspecies at the molecular level. Moreover, take Lateolabrax maculates and Epinephelus coioides as outgroups, molecular phylogenetic tree showed that all the h...
Faiz Muhammad1,2, Canfeng Dou1, Zhen-ming Lü1,*, Li Gong1, Xun Du1 and Muhammad Shafi3
...subunit ATPase 6, thirty haplotypes and 140 polymorphic sites were noted, whereas (0.740, 0.048) high and low haplotype and nucleotide diversity observed. The data was further tested with AMOVA that validates 91.24% variation among populations and 8.76% within population. Genetic fixation index was also calculated as 0.91243*. The neighbor-joining phylogenetic analysis revealed three lineages. The Dongshan population distinctly has shown separate lineage....
Zhen-Yang Wu1, Guang-Xin E2,*, Hui Ran1, Da-Hui Wang1 and Tian-You Yang1
...nformative sites, and 18 haplotypes were detected. The number of haplotypes within populations ranged from one (WS and DJ) to six (JK). Haplotype diversity ranged from 0.000 (DJ and WS) to 0.793 (JK). The largest amount of nucleotide diversity was found in the SQ population (0.03111 ), whereas the smallest amount was in the DJ and WS (0.00000) populations. Phylogenetic analysis revealed that these 10 populations could be sep...
Zhaochao Deng1, Jingchen Chen1, Na Song2, Yongzhen Li3 and Zhiqiang Han1,*
...were obtained defining 7 haplotypes in the South China Sea population. Contrary to heterogeneous expectation, AMOVA and pairwise FST values showed that the genetic differences in this region were all non-significant. The pattern of population demography showed a stable model in this species in the South China Sea population. To reveal its population structure within the large-scale geography distribution, we added 169 sequences of the mitocho...
Zhaochao Deng1, Na Song2, Yongzhen Li3, Tianxiang Gao1 and Zhiqiang Han1,*
...ere obtained defining 39 haplotypes. Based on the NJ tree, two distinct lineages were detected, with strong frequency differences in the geographical distribution. Both lineages were found in Xisha and Zhongsha archipelagos, but only one lineage (lineage B) was detected in Nansha archipelago. Contrary to homogenization expectation, AMOVA and pairwise FST values showed that the genetic differences among three archipelagos were all significant....
SiRui Wang1,2, Fekede Regasa Joka1,2, XiaoLong Wang1,2,* and SuYing Bai2,*
...d by PCR sequencing. The haplotypes were analysed by DNA SP software. The Datamonkey Adaptive Evolution Server was used to detect the selection pressure. Phylogenetic analyses of the reported sequences of jungle fowl (Gallus gallus) and the 10 tested birds were performed. A total of 10 nucleotide sequences of the GED region of the Mx gene in wild birds were obtained, with a length of 231 bp, encoding 77 amino acids. The third locus in all tested ...
Bingbing Gao1, Na Song1, Zhonglu Li2, Tianxiang Gao3 and Liqin Liu3,*
... 26 mutation loci and 27 haplotypes were detected. All six populations were characterized by low haplotype diversity (0.39–0.59) and low nucleotide diversity (0.00038–0.00073). The result of AMOVA and pairwise Fst values indicated weak or no genetic differentiation among different populations. Haplotype network and NJ phylogenetic trees revealed that there was no distinctly geographical distribution pattern among the
Tasleem Akhtar1,2,Ghazanfar Ali1,*, Nuzhat Shafi2 and Abdul Rauf2
...m 1527 to 1552 bps. Five haplotypes (h) were observed, with haplotype diversity (Hd) 0.5323±0.080. Among 5 haplotypes, 2, 2 and 1 haplotype were detected in S. plagiostomus, S. niger and S. esocinus, respectively. Haplotype diversity was lowest and same in S. esocinus, S. niger and S. progastus (0.0001) and highest in S. plagiostomus (0.5436). Average number of nucleotide differences...
Peng Ren1, Xian-Qing Liu1, Chao-Wu Yang2,3, Hua-Rui Du2,3, Xiao-Song Jiang2,3 and Yi-Ping Liu1*
...rences were found in the haplotypes of SNP1 and SNP2 (P>0.05). These results suggest that SNP4 (A4812316G) in the 3’-UTR of the MyD88 gene is linked to genetic resistance to Salmonella Pullorum infection and may provide an important reference for the marker-assisted selection of chickens during disease-resistance breeding.
...
Muhammad Younis Laghari1,2, Zixia Zhao1, Yiwen Gong3, Punhal Lashari1,2, Shangqi Li1, Jian Xu1 , Ateeque Rahman Khooharo4, Jiongtang Li1,* and Yan Zhang1*
...lymorphic, including six haplotypes with an average sequence divergence of 11.03% (SE = 0.78%). Four haplotypes (MF177501-MF177504) were shared in these four population. However, two specific haplotypes (MF177499-MF177500) were only observed in Hainan population. To simplify procedure and improve effectiveness of identifying the Hainan population, one specific PCR-based marker acted as IND...
Jiantong Feng, Xueping Wen, Yahong Guo, Yingying Ye*, Jiji Li and Baoying Guo
...Results revealed that 33 haplotypes were defined in COIII gene, and 30 haplotypes were defined in 12S rRNA gene. The pairwise Fst values between the ZS population and other four populations were range from 0.122~0.154 (COIII, P< 0.05) and 0.052~0.228 (12S rRNA, P<0.05), respectively. The revealed that ZS population was significant divergence from other four populations, and no significan...
Peimin Yang*, Zongyun Hu, Yixin Liu, Guanghai Jin and Lei Wang
...polymorphic sites and 20 haplotypes among five populations, and the samples exhibited high haplotype diversity (h=0.8467) and low nucleotide diversity (Pi=0.0063). Genetic distances ranged from 0.0002 to 0.0149 within and 0.0007 to 0.0140 between populations. AMOVA analysis indicated significant genetic differentiation among populations (Fst=0.3202, P<0.01) and 68.98% of the total variation was resulted from...
Guang-Hui Tan, Yi-Yu Zhang*, Yuan-Yu Qin, Lei Wu and Jie-Zhang Li
...ity, respectively. Three haplotypes and six diplotypes were identified by the combination of two SNPs. Diplotypes had dominantly affected on tested lipid indexes except for IMF. Diplotype H1H1 was advantageous for the improvement of meat quality. Therefore, our data suggested that two novel SNPs: CDS 216 A>G and CDS 681 T>A in CYP7A1 gene were potential candidate markers for improving meat quality. It also provides reference data for early breeding and s...
Yan Zhou1,2, Hai Xia Han1,2, Qiu Xia Lei1,2, Jin Bo Gao1,2, Wei Liu1,2, Fu Wei Li1,2, Jie Liu1,2 and Ding Guo Cao1,2*
...duction in chickens, the haplotypes and diplotypes based on three genetic mutations (NC_006127.2:g.8467G>A, NC_006127.2:g.12321G>A and NC_006127.2:g.13876A>G) were constructed, and the associations of diplotypes with reproduction traits were assessed, their effects on gene expression were evaluated also. As a result, three haplotypes H1 (G-G-A), H2 (G-G-G) and H3 (A-A-G) were obtained, H1 was the main haplotype with...
Muhammad Umer Khan1,2*, Muhammad Farooq Sabar1, Atif Amin Baig3, Arif-un-Nisa Naqvi4 and Muhammad Usman Ghani1
... A total of 75 different haplotypes were identified in Shin people; among them, 72 were unique and 3 were shared by more than one individual. This study revealed the predominance of West Eurasian lineages in the Shin population (59.49%), followed by South Asian lineages (25.32%) and then East and Southeast Asian lineages (15.19%). Shin population presented a high genetic diversity of 0.9996 and a low random match probability of 0.0129. To the best of our knowl...
Ehsan Kashani1, Hamid Reza Rezaei2*, Morteza Naderi3 and Nematolah Khorasani4
...lades without any common haplotypes. Long-eared specimens grouped in two distinct phylogenetic groups which belong to two different geographic areas while for P. hypomelas no significant divergence happened in the species life history.
...
Shuanping Zhao, Lei Xu, Hai Jin and Yutang Jia*
... total of four different haplotypes were constructed and the frequency of the main haplotypes AAG accounted for over 61.2 % of the total individuals. Association analysis indicated that all of the three SNPs were significantly associated with growth traits in the detected population. Furthermore, real-time PCR indicated that CFL2 mRNA was varied expressed in all studied tissues. The results of our study provide eviden...
Yongyun Zhang1, 2, Xinyang Fan1, Fangting Zhou1, Weizhen Li3, Yina Ouyang1,4 and Yongwang Miao1*
...ht buffalo CSN1S1 haplotypes were defined in this study, and accordingly, 6 protein variants and 2 synonymous variants of αS1-CN were inferred and named. The variants A, B’, B’’, C, E and F were observed only in river buffalo, whereas variant D was found only in swamp buffalo. The variant B was shared by both types of buffalo with high frequencies. The buffalo variants determined here did not exist in Bos...
Aiguo Zhou1,2, Di Sun1,2,Shulin Liu 1,2, Yongyong Feng1,2, Yue Zhang3,
Yanfeng Chen4, Shaolin Xie1,2* and Jixing Zou1,2*
...wed that there were nine haplotypes in 60 individuals, which were eight unique and one shared haplotypes. In addition, the genetic distance for inter-species of all the haplotypes ranged from 0.000 to 0.004. And the mean pair-wise genetic distance between the two color morphs were estimated to be 0.001. This indicated that the “Bicolor” and “White” types of northern...
Xuhai Wang1,2, Xin Li1, Fangyuan Yuan1, Chaocheng Li1, Bin Jia1* and Song Jiang1*
...nt and non-resistant MHC haplotypes after oral infection with E. granulosus eggs. The results demonstrated that miR-216b negatively regulated IL2RB in the cystic echinococcosis intestinal tissues, and they were differentially expressed in the intestine tissue between the resistant sheep and non-resistant sheep, more widely distributed in the resistant group. These results illustrated that miR-216b and IL2RB activated stronger immune response in the resi...
Xiaoyun He1, Yongfu La2, Jinxin Wang1, Ran Di1, Qiuyue Liu1, Xiangyu Wang1, Wenping Hu1 and Mingxing Chu1*
...lt;0.01). The results of haplotypes analysis indicated that H2, H7 were preponderant haplotype in high prolificacy sheep breed. The litter size of TT genotype was significantly higher than that in CC genotype at T1235C loci in STH sheep (P<0.05). The current study provides evidence in sheep for genetic markers that might be used in breeding program.
...
Shahid Sherzada1,2*, Muhammad Naeem Khan1 and Masroor Ellahi Babar2
... polymorphic sites and 4 haplotypes. Mean haplotypes and nucleotide diversity was 0.42 and 0.0018, respectively. The mean intraspecific and intragenric K2P genetic distances were 0.2% and 1.2%, respectively. Rate of transitional and transversional substitution was 16.68% and 4.16%, respectively. The transition/transversion bias value R was 1.25. The negative values of Tajima D test as well as Fu and Li D and F tests supporte...
Asli Salcioglu
...w three distinct Spicara haplotypes/haplogroups, corresponding to three different species. Additionally, the number of mutations and high values of sequence divergences were useful in differentiating the three different Spicara....
Abida Shehzadi*, Muhammad Shafique and Ahmad Ali Shahid
...ecognition of 124 unique haplotypes with diversity value of 0.996. Locus DYS385a/b demonstrated highest power of discrimination, polymorphism information content and gene diversity as 0.907, 0.854 and 0.807 respectively. Analysis of Molecular Variance (AMOVA) and multidimensional scaling plot (MDS) were also generated by using online tools at YHRD database. The data from this study could have significant importance in forensic applications, population studies ...
Weidong Huang1,2,3, Xinyue Liang1,2,3, Xiufeng Xie4, Xingmin Wang2, 3 and Xiaosheng Chen1,2,3*
... addition, the number of haplotypes was 17 and the same elytral color patterns of M. sexmaculatus didn’t share the same haplotype. Furthermore, phylogenetic analyses showed all M. sexmaculatus samples formed a single clade, but the identical elytral pattern individuals do not cluster together as no special relationships among different phenotypes individuals. Our systematic analyses illustrated the same elytral forms of M. sexmaculatus do not possess clo...
Ngoc Tan Nguyen1*, Minh Thanh Tram1, Thi Thu Pham1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Nguyen Khang Duong4
...re transversion, with 21 haplotypes observed. Nucleotide and haplotype diversity indices (π and Hd) were 0.03005 and 0.889, respectively. The genetic diversity of Saanen goats was highest at (π) = 0.03031 and (Hd) = 0.987, while the lowest genetic diversity was found in Bach Thao goats (π = 0.00089 and Hd = 0.533). Genetic distance between WB and CO or BT was higher (0.058) than between RB and CO or BT (0.056 or 0.055). The lowest genetic distance was...
Ngoc Tan Nguyen1*, Pham Kim Ngan Nguyen1, Thao Huong Phan1, Tan Loi Le1, Thi Khanh Ly Nguyen1, Tuan Thanh Hoang2, Cong Thieu Pham3, Cong Dinh Nguyen3, Nguyen Khang Duong4
...polymorphic sites and 26 haplotypes were observed. Nucleotide and haplotype diversity index (π and Hd) were 0.06267 and 0.987, respectively. Genetic distance among swamp buffalo populations was smaller (ranging 0.050-0.056) than between Murrah and the swamp buffalo populations (ranging 0.091-0.125). Among the three native Vietnamese buffalo groups, the genetic distance between Bao Yen and LangBiang (0.050) buffalo populations was smaller than between Thanh ...
He-Cai Zhang, Tian-Ge Hu, Chang-Ying Shi, Guang-Wen Chen* and De-Zeng Liu
...e results showed that 46 haplotypes were detected in total, including 10 shared haplotypes and 36 private ones. The overall haplotype diversity (Hd) and nucleotide diversity (π) were 0.961 and 0.00157, respectively. The phylogenetic relationship and haplotype network analysis indicated that there was no obvious correspondence between the haplotypes and the geographical locations, reveal...
Nasir Ali1,2,6, Muhammad Ilyas2,3, Nazia Akbar1,2*, Gohar Rahman2, Shakirullah Khan4, Mujaddad Ur Rehman6, Abdul Samad5, Habib Ahmad1,2 and Bibi Nazia Murtaza7*
...ults revealed 25% unique haplotypes in ancient samples whereas 28% unique haplotypes have been observed in the modern samples. The most frequent haplotype found was H2a (23% in ancient and 10% in modern samples). Our results show that with the exception of ancient Dir, there are genetic similarities among the ancient lines between Hazara, Chitral and Swat. It revealed that most of the ancient and modern samples belong to the...
Perinçek Seçkinozan Seker
...iversity. A total of two haplotypes were identified for cyt b, while three haplotypes were identified for COI. Of the haplotypes detected, two cyt b and two COI haplotypes were specific to Turkey. Molecular phylogenetic analyses; Maximum Likelihood (ML), Bayesian Inference (BI), and Network revealed topologies and evolutionary networks which were not def...
Chengrui Yan1, Jing Miao1, Jiantong Feng1, Liping Xia1, Yingying Ye1,2*, Jiji Li1 and Baoying Guo1,2
... TOP, SLP, and SUND) and haplotypes indicated that SLP and SUND carried highest influence on the haplotype distribution. SKT and total precipitation TOP were highly correlated with haplotype formation. Combine life story of T. clavigera revealed that environmental factors contribute to the nuances of population genetic in different regions. Understanding the genetic variation and population structure of T. clavigera populations along the coast of China Sea obt...
Iqra Almas, Samia Afzal*, Muhammad Idrees, Muhammad Shahid, Iram Amin and Kausar Malik
...ere shown more number of haplotypes and total diversity as compared to sons. The quasispecies analysis showed the mother and sons were infected with HBV having similar genetic makeup, indicating the vertical transfer of infection. This case study provides knowledge about genetic variations that contributes to the improved diagnosis of the infection, treatment therapy, follow-up, and future treatment strategies....
Rongrong Wang1,2, Da Ji1,2, Junjie Yao1,2*, Wenzheng Zhang1,2, Xianjun Zhou1,2, Xin Su1,2 and Tianquan Bai3
...dividuals displayed four haplotypes, and the overall haplotype diversity (Hd) and nucleotide diversity (Pi) of the three C. sowerbyi groups were 0.531 and 0.00067, respectively. Analysis of molecular variance (AMOVA) showed that inter- and intrapopulation variation accounted for 41.63039% and 58.36961%, respectively, of the total variation, and the genetic variation coefficient (Fst) was 0.05268. The gene flow (Nm) values between the three C. sowerbyi populati...
Nguyen Ba Trung1,2*, Pham Thi Kim Phuong1,2
Nguyen Ba Trung1,2*, Pham Thi Kim Phuong1,2
