Pub Date : 2019-11-25DOI: 10.1080/24701394.2019.1694015
M. A. Phukuntsi, M. du Plessis, D. Dalton, R. Jansen, F. Cuozzo, M. Sauther, A. Kotzé
Abstract Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species’ most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007–0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166–0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2–3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3–5 in coding region and 6–10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.
{"title":"Population genetic structure of the thick-tailed bushbaby (Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions","authors":"M. A. Phukuntsi, M. du Plessis, D. Dalton, R. Jansen, F. Cuozzo, M. Sauther, A. Kotzé","doi":"10.1080/24701394.2019.1694015","DOIUrl":"https://doi.org/10.1080/24701394.2019.1694015","url":null,"abstract":"Abstract Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species’ most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007–0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166–0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2–3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3–5 in coding region and 6–10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"30 1","pages":"1 - 10"},"PeriodicalIF":0.0,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74101165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-17DOI: 10.1080/24701394.2019.1693552
Sameer M. Padhye, N. Dahanukar
{"title":"Methodological flaws overshadow the evidence for a species complex in Indialona ganapati (Chydoridae)","authors":"Sameer M. Padhye, N. Dahanukar","doi":"10.1080/24701394.2019.1693552","DOIUrl":"https://doi.org/10.1080/24701394.2019.1693552","url":null,"abstract":"","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"9 1","pages":"880 - 881"},"PeriodicalIF":0.0,"publicationDate":"2019-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78485149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-17DOI: 10.1080/24701394.2019.1693550
C. Kunprom, P. Pramual
Abstract Fruit flies (Diptera: Tephritidae) are significant insect pests of many commercially important fruits and vegetables. Therefore, rapid and accurate species identification methods are required for the regulation, management and quarantine of these pests. In this study, we examined the efficiency of mitochondrial cytochrome c oxidase I sequences for species identification of fruit flies in Thailand. Data analyses based on 42 fruit fly taxa revealed moderate performance of this genetic marker. There were 14 taxa that have no barcode gap and thus could not be identified unambiguously to species by this methodology. Taxonomic uncertainty, inadequate variation of the marker and misidentifications of specimens deposited in the public database are the most likely factors explaining unsuccessful identification. DNA barcodes also revealed cryptic diversity in five taxa (Bactrocera caudata, B. tuberculata, B. infesta, Zeugodacus isolatus, Carpomya vesuviana). These species require further taxonomic investigation of if they are different cryptic taxa or are indications of geographic structuring of within single species.
{"title":"DNA barcoding of fruit flies (Diptera: Tephritidae) in Thailand: ambiguity, misidentification and cryptic diversity","authors":"C. Kunprom, P. Pramual","doi":"10.1080/24701394.2019.1693550","DOIUrl":"https://doi.org/10.1080/24701394.2019.1693550","url":null,"abstract":"Abstract Fruit flies (Diptera: Tephritidae) are significant insect pests of many commercially important fruits and vegetables. Therefore, rapid and accurate species identification methods are required for the regulation, management and quarantine of these pests. In this study, we examined the efficiency of mitochondrial cytochrome c oxidase I sequences for species identification of fruit flies in Thailand. Data analyses based on 42 fruit fly taxa revealed moderate performance of this genetic marker. There were 14 taxa that have no barcode gap and thus could not be identified unambiguously to species by this methodology. Taxonomic uncertainty, inadequate variation of the marker and misidentifications of specimens deposited in the public database are the most likely factors explaining unsuccessful identification. DNA barcodes also revealed cryptic diversity in five taxa (Bactrocera caudata, B. tuberculata, B. infesta, Zeugodacus isolatus, Carpomya vesuviana). These species require further taxonomic investigation of if they are different cryptic taxa or are indications of geographic structuring of within single species.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"28 1","pages":"861 - 873"},"PeriodicalIF":0.0,"publicationDate":"2019-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90211636","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-17DOI: 10.1080/24701394.2019.1693549
Pavitchaya Koolkarnkhai, Chidchanok Intakham, Pradit Sangthong, Wunrada Surat, P. Wonnapinij
Abstract Mitochondrial DNA (mtDNA) sequences, especially mitochondrial control region (mtCR) and mitochondrial cytochrome c oxidase subunit I (mtCOI), have been widely used in population and evolutionary genetic analyses of metazoan. The presence of mtDNA heteroplasmy – a mixture of mtDNA haplotypes – possibly affects these analyses. This study aimed to reveal mtDNA heteroplasmy in mtCR, mtCOI, and mtND2 (mitochondrial NADH dehydrogenase subunit 2) of Portunus pelagicus, and examine its effect on the use of mtCR and mtCOI sequences. The screening result showed that the probability of observing mtDNA heteroplasmy was approximately 8%. Across the three targeted regions, 92 heteroplasmic variants were observed from seven samples comprising three mothers and four offspring. Most inherited heteroplasmy presented transition and silence mutation. By comparing the proportion of shared variants among maternal relatives to that among non-relatives, the result suggested that most heteroplasmic variants observed in an individual are inherited. Statistical analyses carried out on the inter-generational differences suggested that random drift and purifying selection play roles in determining the offspring’s heteroplasmy level. The size of the random shift varies according to the location of variants and the mothers. The phylogenetic analysis showed that the presence of mtDNA heteroplasmy in mtCR and mtCOI does not affect familial and species identification, respectively. This study firstly reported the mtDNA heteroplasmy in P. pelagicus, its inheritance pattern, and its effect on the use of mtDNA sequence data. This basic knowledge would be useful for the study based on mtDNA sequence data, especially in other invertebrates.
{"title":"Portunus pelagicus mtDNA heteroplasmy inheritance and its effect on the use of mtCR and mtCOI sequence data","authors":"Pavitchaya Koolkarnkhai, Chidchanok Intakham, Pradit Sangthong, Wunrada Surat, P. Wonnapinij","doi":"10.1080/24701394.2019.1693549","DOIUrl":"https://doi.org/10.1080/24701394.2019.1693549","url":null,"abstract":"Abstract Mitochondrial DNA (mtDNA) sequences, especially mitochondrial control region (mtCR) and mitochondrial cytochrome c oxidase subunit I (mtCOI), have been widely used in population and evolutionary genetic analyses of metazoan. The presence of mtDNA heteroplasmy – a mixture of mtDNA haplotypes – possibly affects these analyses. This study aimed to reveal mtDNA heteroplasmy in mtCR, mtCOI, and mtND2 (mitochondrial NADH dehydrogenase subunit 2) of Portunus pelagicus, and examine its effect on the use of mtCR and mtCOI sequences. The screening result showed that the probability of observing mtDNA heteroplasmy was approximately 8%. Across the three targeted regions, 92 heteroplasmic variants were observed from seven samples comprising three mothers and four offspring. Most inherited heteroplasmy presented transition and silence mutation. By comparing the proportion of shared variants among maternal relatives to that among non-relatives, the result suggested that most heteroplasmic variants observed in an individual are inherited. Statistical analyses carried out on the inter-generational differences suggested that random drift and purifying selection play roles in determining the offspring’s heteroplasmy level. The size of the random shift varies according to the location of variants and the mothers. The phylogenetic analysis showed that the presence of mtDNA heteroplasmy in mtCR and mtCOI does not affect familial and species identification, respectively. This study firstly reported the mtDNA heteroplasmy in P. pelagicus, its inheritance pattern, and its effect on the use of mtDNA sequence data. This basic knowledge would be useful for the study based on mtDNA sequence data, especially in other invertebrates.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"23 1","pages":"848 - 860"},"PeriodicalIF":0.0,"publicationDate":"2019-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77232291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-11DOI: 10.1080/24701394.2019.1687693
S. Ishar, Kiroobhashini Parameswaran, Nur Safrina Masduki, Rus Dina Rus Din
Abstract DNA variations are alterations found in DNA sequence, occurring in both nuclear DNA and mitochondrial DNA. Variations might differ in individual following population, respectively. The aim of this study was to find variations in target sequence of mtDNA (16000–16200) to be used as marker in Malay and Chinese population. A total of 30 buccal swab samples from 20 Malay and 10 Chinese subjects were collected and preserved on FTA card. The FTA card that contained DNA sample was punched to be included into polymerase chain reaction mixture. Amplification was carried out and the products were sequenced. Sequence variations were found in both Malay and Chinese populations. A total of nine variations (16129, 16108, 16162, 16172, 16148, 16127, 16173, 16099 and 16100) were found in Malay population while a total of seven variations (16129, 16104, 16111, 16109, 16164, 16170 and 16136) were found in Chinese population. Nucleotide position 16129 was found as variation in both Malay and Chinese populations. This study implies that np 16129 can be used as a marker for Malaysian population. For further investigation, the length of the target sequence may be increased to obtain more variations that can be used as markers. This will increase the discrimination power of Malaysian population.
{"title":"Variations in mitochondrial DNA control region among Malay and Chinese subpopulations (sequence 16000–16200)","authors":"S. Ishar, Kiroobhashini Parameswaran, Nur Safrina Masduki, Rus Dina Rus Din","doi":"10.1080/24701394.2019.1687693","DOIUrl":"https://doi.org/10.1080/24701394.2019.1687693","url":null,"abstract":"Abstract DNA variations are alterations found in DNA sequence, occurring in both nuclear DNA and mitochondrial DNA. Variations might differ in individual following population, respectively. The aim of this study was to find variations in target sequence of mtDNA (16000–16200) to be used as marker in Malay and Chinese population. A total of 30 buccal swab samples from 20 Malay and 10 Chinese subjects were collected and preserved on FTA card. The FTA card that contained DNA sample was punched to be included into polymerase chain reaction mixture. Amplification was carried out and the products were sequenced. Sequence variations were found in both Malay and Chinese populations. A total of nine variations (16129, 16108, 16162, 16172, 16148, 16127, 16173, 16099 and 16100) were found in Malay population while a total of seven variations (16129, 16104, 16111, 16109, 16164, 16170 and 16136) were found in Chinese population. Nucleotide position 16129 was found as variation in both Malay and Chinese populations. This study implies that np 16129 can be used as a marker for Malaysian population. For further investigation, the length of the target sequence may be increased to obtain more variations that can be used as markers. This will increase the discrimination power of Malaysian population.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"75 1","pages":"843 - 847"},"PeriodicalIF":0.0,"publicationDate":"2019-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85778061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-11-07DOI: 10.1080/24701394.2019.1687691
A. Zubaer, Alvan Wai, G. Hausner
Abstract An intron landscape was prepared for the fungal mitochondrial nad5 gene. A hundred and eighty-eight fungal species were examined and a total of 265 introns were noted to be located in 29 intron insertion sites within the examined nad5 genes. Two hundred and sixty-three introns could be classified as group I types and two group II introns were noted. One additional group II intron module was identified nested within a composite group I intron. Based on features related to RNA secondary structures, introns can be classified into different subtypes and it was observed that intron insertion-sites are biased towards phase 0 and they appear to be specific to an intron type. Intron landscapes could be used as a guide map to predict the location of fungal mtDNA mobile introns, which are composite elements that include a ribozyme component and in some instances open reading frames encoding homing endonucleases or reverse transcriptases and all of these have applications in biotechnology.
{"title":"The fungal mitochondrial Nad5 pan-genic intron landscape","authors":"A. Zubaer, Alvan Wai, G. Hausner","doi":"10.1080/24701394.2019.1687691","DOIUrl":"https://doi.org/10.1080/24701394.2019.1687691","url":null,"abstract":"Abstract An intron landscape was prepared for the fungal mitochondrial nad5 gene. A hundred and eighty-eight fungal species were examined and a total of 265 introns were noted to be located in 29 intron insertion sites within the examined nad5 genes. Two hundred and sixty-three introns could be classified as group I types and two group II introns were noted. One additional group II intron module was identified nested within a composite group I intron. Based on features related to RNA secondary structures, introns can be classified into different subtypes and it was observed that intron insertion-sites are biased towards phase 0 and they appear to be specific to an intron type. Intron landscapes could be used as a guide map to predict the location of fungal mtDNA mobile introns, which are composite elements that include a ribozyme component and in some instances open reading frames encoding homing endonucleases or reverse transcriptases and all of these have applications in biotechnology.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"33 1","pages":"835 - 842"},"PeriodicalIF":0.0,"publicationDate":"2019-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74004453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-10-01DOI: 10.1080/24701394.2019.1670820
Xiaomeng Zhang, Xiumei Zhang, N. Song, T. Gao, Linlin Zhao
Abstract Sillago aeolus is a species from Sillaginidae, which is a widely distributed species with important scientific and economic value in the coast of China. Its population genetics have not been studied. This study investigated the population genetics of S. aeolus in the eastern and southern coast of China based on the mitochondrial control region markers obtained from 248 individuals of 9 locations. The population was characterized by a high population diversity with a low nucleotide diversity. There were no branches corresponding to the sampling sites according to the haplotype network and NJ tree. Recent asymmetric gene flow exchanges and significant genetic differences were detected between the Haikou population and the other populations. AMOVA result indicated slight genetic structures with homogeneity suggested. The neutral test and the mismatch distribution revealed a recent population expansion event. Historical geographic events may be the reason for the homogeneity within the population.
{"title":"Study on population genetics of Sillago aeolus (Perciformes: Sillaginidae) in the Coast of China","authors":"Xiaomeng Zhang, Xiumei Zhang, N. Song, T. Gao, Linlin Zhao","doi":"10.1080/24701394.2019.1670820","DOIUrl":"https://doi.org/10.1080/24701394.2019.1670820","url":null,"abstract":"Abstract Sillago aeolus is a species from Sillaginidae, which is a widely distributed species with important scientific and economic value in the coast of China. Its population genetics have not been studied. This study investigated the population genetics of S. aeolus in the eastern and southern coast of China based on the mitochondrial control region markers obtained from 248 individuals of 9 locations. The population was characterized by a high population diversity with a low nucleotide diversity. There were no branches corresponding to the sampling sites according to the haplotype network and NJ tree. Recent asymmetric gene flow exchanges and significant genetic differences were detected between the Haikou population and the other populations. AMOVA result indicated slight genetic structures with homogeneity suggested. The neutral test and the mismatch distribution revealed a recent population expansion event. Historical geographic events may be the reason for the homogeneity within the population.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"10 1","pages":"825 - 834"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72878345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-09-28DOI: 10.1080/24701394.2019.1670819
Thanadon Dokrungkoon, Preyaporn Onsod, Prapatsorn Areesirisuk, B. Rerkamnuaychoke, K. Vanikieti, T. Chareonsirisuthigul
Abstract Leber hereditary optic neuropathy (LHON) causes painless vision loss resulting from mitochondrial DNA (mtDNA) mutation. Over 95% of LHON cases result from one of three mtDNA point mutations (m.3460G>A, m.11778G>A, and m.14484T>C). There is no established cure for LHON; early and accurate diagnosis would enable patients to be given appropriate treatments leading to a reduction of the disease progression. To increase the accessibility to molecular genetic testing for LHON, an accurate and cost-effective technique is required. The purpose of this study was to evaluate the accuracy of multiplex ligation-dependent probe amplification (MLPA) for detecting the three common mutations in 18 LHON blood specimens. Validation of the results using direct DNA sequencing technology proved that the MLPA technique had 100% accuracy, with no false-positive results. This study demonstrates that MLPA could provide a highly accurate, economical, and widely accessible technique for routine molecular genetic testing for mitochondrial disorders.
{"title":"Performance of the MLPA technique for detecting common mutations in Leber hereditary optic neuropathy","authors":"Thanadon Dokrungkoon, Preyaporn Onsod, Prapatsorn Areesirisuk, B. Rerkamnuaychoke, K. Vanikieti, T. Chareonsirisuthigul","doi":"10.1080/24701394.2019.1670819","DOIUrl":"https://doi.org/10.1080/24701394.2019.1670819","url":null,"abstract":"Abstract Leber hereditary optic neuropathy (LHON) causes painless vision loss resulting from mitochondrial DNA (mtDNA) mutation. Over 95% of LHON cases result from one of three mtDNA point mutations (m.3460G>A, m.11778G>A, and m.14484T>C). There is no established cure for LHON; early and accurate diagnosis would enable patients to be given appropriate treatments leading to a reduction of the disease progression. To increase the accessibility to molecular genetic testing for LHON, an accurate and cost-effective technique is required. The purpose of this study was to evaluate the accuracy of multiplex ligation-dependent probe amplification (MLPA) for detecting the three common mutations in 18 LHON blood specimens. Validation of the results using direct DNA sequencing technology proved that the MLPA technique had 100% accuracy, with no false-positive results. This study demonstrates that MLPA could provide a highly accurate, economical, and widely accessible technique for routine molecular genetic testing for mitochondrial disorders.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"76 1","pages":"819 - 824"},"PeriodicalIF":0.0,"publicationDate":"2019-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86739698","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-09-23DOI: 10.1080/24701394.2019.1659250
Shun-Gang Chen, Ji Li, Fan Zhang, Bo Xiao, Jiaming Hu, Yin-Qiu Cui, M. Hofreiter, X. Hou, Guilian Sheng, Xulong Lai, Junxia Yuan
Abstract Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290–1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117–222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.
{"title":"Different maternal lineages revealed by ancient mitochondrial genome of Camelus bactrianus from China","authors":"Shun-Gang Chen, Ji Li, Fan Zhang, Bo Xiao, Jiaming Hu, Yin-Qiu Cui, M. Hofreiter, X. Hou, Guilian Sheng, Xulong Lai, Junxia Yuan","doi":"10.1080/24701394.2019.1659250","DOIUrl":"https://doi.org/10.1080/24701394.2019.1659250","url":null,"abstract":"Abstract Domestic Bactrian camel (Camelus bactrianus) used to be one of the most important livestock species in Chinese history, as well as the major transport carrier on the ancient Silk Road. However, archeological studies on Chinese C. bactrianus are still limited, and molecular biology research on this species is mainly focused on modern specimens. In this study, we retrieved the complete mitochondrial genome from a C. bactrianus specimen, which was excavated from northwestern China and dated at 1290–1180 cal. years before present (yBP). Phylogenetic analyses using 18 mitochondrial genomes indicated that the C. bactrianus clade was divided into two maternal lineages. The majority of samples originating from Iran to Japan and Mongolia belong to subclade A1, while our sample together with two Mongolian individuals formed the much smaller subclade A2. Furthermore, the divergence time of these two maternal lineages was estimated as 165 Kya (95% credibility interval 117–222 Kya), this might indicate that several different evolutionary lineages were incorporated into the domestic gene pool during the initial domestication process. Bayesian skyline plot (BSP) analysis suggest a slow increase in female effective population size of C. bactrianus from 5000 years ago, which corresponds to the beginning of domestication of C. bactrianus. The present study also revealed that there were extensive exchanges of genetic information among C. bactrianus populations in regions along the Silk Road.","PeriodicalId":54298,"journal":{"name":"Mitochondrial Dna Part a","volume":"59 1","pages":"786 - 793"},"PeriodicalIF":0.0,"publicationDate":"2019-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88253685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-09-17DOI: 10.1080/24701394.2019.1665036
E. Françoso, A. Zuntini, P. Ricardo, J. P. Silva, R. Brito, B. Oldroyd, M. C. Arias
Abstract Tetragonula carbonaria, Tetragonula davenporti, Tetragonula hockingsi and Tetragonula mellipes comprise a species complex of Australian stingless bee species known as the ‘Carbonaria’ group. The species are difficult to distinguish morphologically and the major species-defining characters relate to comb architecture and nest entrance ornamentation. The taxonomy of the group is further complicated by likely nuclear mitochondrial pseudogenes (numts) and inter-specific hybrids. Here we demonstrate the existence of COI numts and isolate and characterize the ‘true’ mt-COI gene in T. carbonaria and T. hockingsi. Numts were isolated from enriched-nuclear DNA extraction followed by PCR amplification and Sanger sequencing, and were recognized by the presence of deletions and/or premature stop codons in the translated sequences. The mt-COI sequences were obtained from NGS sequencing using purified mtDNA. In T. carbonaria, two numts (numt1 and numt2) were identified and a third (numt3) was identified in T. hockingsi. Numt2 and numt3 are similar (1.2% sequence divergence), indicating a recent common origin. The genetic distance between the mt-COI of the two Tetragonula species was higher than might be expected for closely related species, 16.5%, corroborating previous studies in which T. carbonaria and T. hockingsi were regarded as separate species. The three numts are more similar to the COI of other stingless bee species, including Australian Austroplebia australis and South American Melipona bicolor (81.7–83.9%) than to the mt-COI of their own species (70–71.4%). This is because the mt-COI of T. carbonaria and T. hockingsi differ greatly from other Meliponinae. Our findings explain some formerly puzzling aspects of Carbonaria biogeography, and misinterpreted amplifications.
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