Maira A Rizo-Fuentes, Camilo A Correa-Cárdenas, Carlos A Lasso, Mónica A Morales-Betancourt, Dalia C Barragán-Barrera, Susana Caballero
{"title":"Phylogeography, genetic diversity and population structure of the freshwater stingray, <i>Paratrygon aiereba</i> (Müller & Henle, 1841) (Myliobatiformes: Potamotrygonidae) in the Colombian Amazon and Orinoco basins.","authors":"Maira A Rizo-Fuentes, Camilo A Correa-Cárdenas, Carlos A Lasso, Mónica A Morales-Betancourt, Dalia C Barragán-Barrera, Susana Caballero","doi":"10.1080/24701394.2020.1844679","DOIUrl":"https://doi.org/10.1080/24701394.2020.1844679","url":null,"abstract":"<p><p>The freshwater stingray <i>Paratrygon aiereba</i> have coloration, osteological and morphometric variations that could suggest the existence of more than one species in Colombia. In order to evaluate the phylogeography, population structure and genetic diversity for <i>P. aiereba</i> distributed in the Amazon and Orinoco basins, we amplified <i>Cytochrome oxidase subunit 1 (COI)</i> partial region of mitochondrial DNA (<i>mtDNA</i>) in 50 samples from eight different sub-basins. Our results suggest three phylogroups and a vicariance event occurred 43 million years ago proposing how <i>Paratrygon</i> diverged into the basins. A high population structure (<i>Φ<sub>ST</sub></i> = 0.692; <i>p</i> < 0.005) and a value of (<i>K</i>) of 3 were defined. A high genetic diversity within phylogroups was found: Phylogroup A (<i>h</i> = 0.64; π% = 2.48), Phylogroup B (<i>h</i> = 0.552; π% = 1.67), and Phylogroup C (<i>h</i> = 0.49; π% = 0.73). These results should be considered in local management plans, conservation programs and reclassification in at least Amazon and Orinoco.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 1","pages":"20-33"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1844679","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38396493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gabriel Iketani, Luciana Pimentel, Ezequias Dos Santos Torres, Péricles Sena do Rêgo, Iracilda Sampaio
{"title":"Mitochondrial heteroplasmy and pseudogenes in the freshwater prawn, <i>Macrobrachium amazonicum</i> (Heller, 1862): DNA barcoding and phylogeographic implications.","authors":"Gabriel Iketani, Luciana Pimentel, Ezequias Dos Santos Torres, Péricles Sena do Rêgo, Iracilda Sampaio","doi":"10.1080/24701394.2020.1844677","DOIUrl":"https://doi.org/10.1080/24701394.2020.1844677","url":null,"abstract":"<p><p>The mitochondrial cytochrome oxidase c subunit 1 (COI) gene has been widely used in phylogenetic studies of crustaceans and analyses in population genetics. As COI studies have become more popular, there has been an increase in the number of reports of the presence of nuclear insertions of mitochondrial DNA (Numts) and mitochondrial heteroplasmy. Here, we provide evidence of both types of event in the COI sequences of <i>Macrobrachium amazonicum</i>, an economically important freshwater prawn, which is widespread in South America. Heteroplasmy and Numts were confirmed by different methods of DNA extraction (genomic, mitochondrial, and nuclear-enriched DNA), cloning, and sequencing, and were observed in 11 of the 14 populations sampled, primarily in the Amazon region. We discuss how the occurrence of these events affects the interpretation of the genetic relationships among the <i>M. amazonicum</i> populations, and we recommend caution when using COI for genetic inferences in prawns of the genus <i>Macrobrachium</i>, and in particular that any analysis should include nuclear markers.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1844677","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38579331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Analyses of mitogenomic markers shed light on the divergence, population dynamics, and demographic history of Pakistani chickens.","authors":"Sawar Khan, Ayesha Nisar, Habib Ahmad, Sardar Azhar Mehmood, Muddassar Hameed, Xiaochao Zhao, Xiangshu Yang, Xingang Feng","doi":"10.1080/24701394.2020.1845323","DOIUrl":"https://doi.org/10.1080/24701394.2020.1845323","url":null,"abstract":"<p><p>Pakistan is one of a few sites, associated with the earliest known independent domestication event in the evolutionary history of chicken, which is socio-economically and historically the most important poultry bird in the country. However, the divergence, past population dynamics, and demographic history of Pakistani chickens have not been addressed so far. Therefore, we herein investigated the indigenous Pakistani chickens using mitogenomic markers. We first prepared individual DNA samples from the chicken feathers, and generated nucleotide sequence data, which was then subjected to various population genetics analyses. In molecular phylogenetic analysis, the Pakistani chickens were clustered under nine different clades. Among the wild fowls, the Indian red jungle fowl (IRJF) shared very close affinities to Pakistani chickens. The Bayesian skyline plot showed an increase in the effective population size of Pakistani chickens during the last 50 years. Finally, a time-calibrated phylogeny inferred molecular divergence of the Pakistani chickens. A molecular rate of 3.6 × 10<sup>-6</sup> mutations/site/year (95% HPD interval: 2.28 × 10<sup>-8</sup> to 9.32 × 10<sup>-6</sup>) was estimated for the data set. In a rooted tree with root-age of 12058 years (95% HPD interval: 1161-38411), the Pakistani chicken haplotypes showed divergence from IRJF haplotypes around 6987 years (95% HPD interval: 1132-20746) ago, and they shared their most recent common ancestor with <i>Gallus gallus spadiceus</i>, and <i>G. g. jabouillei</i> at the root of the tree. Overall, these results suggest that Pakistani chicken haplotypes share their ancestral gene pool with the IRJF as compared to other red jungle fowl subspecies.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"32 1","pages":"34-42"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1845323","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38592273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Towards understanding the evolutionary dynamics of mtDNA.","authors":"Samuel G Towarnicki, J William O Ballard","doi":"10.1080/24701394.2020.1830076","DOIUrl":"https://doi.org/10.1080/24701394.2020.1830076","url":null,"abstract":"<p><p>Historically, mtDNA was considered a selectively neutral marker that was useful for estimating the population genetic history of the maternal lineage. Over time there has been an increasing appreciation of mtDNA and mitochondria in maintaining cellular and organismal health. Beyond energy production, mtDNA and mitochondria have critical cellular roles in signalling. Here we briefly review the structure of mtDNA and the role of the mitochondrion in energy production. We then discuss the predictions that can be obtained from quaternary structure modelling and focus on mitochondrial complex I. Complex I is the primary entry point for electrons into the electron transport system is the largest respiratory complex of the chain and produces about 40% of the proton flux used to synthesize ATP. A focus of the review is <i>Drosophila</i>'s utility as a model organism to study the selective advantage of specific mutations. However, we note that the incorporation of insights from a multitude of systems is necessary to fully understand the range of roles that mtDNA has in organismal fitness. We speculate that dietary changes can illicit stress responses that influence the selective advantage of specific mtDNA mutations and cause spatial and temporal fluctuations in the frequencies of mutations. We conclude that developing our understanding of the roles mtDNA has in determining organismal fitness will enable increased evolutionary insight and propose we can no longer assume it is evolving as a strictly neutral marker without testing this hypothesis.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"355-364"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1830076","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38464056","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lei Han, Jing-Tong Zhang, Ming-Ming Wang, Ke-Xin Zhu, Xing-Ya Wang
{"title":"Mitochondrial DNA diversity and population structure of <i>Laodelphax striatellus</i> across a broad geographic area in China.","authors":"Lei Han, Jing-Tong Zhang, Ming-Ming Wang, Ke-Xin Zhu, Xing-Ya Wang","doi":"10.1080/24701394.2020.1830075","DOIUrl":"https://doi.org/10.1080/24701394.2020.1830075","url":null,"abstract":"<p><p>The small brown planthopper (SBPH), <i>Laodelphax striatellus</i> Fallén (Hemiptera: Delphacidae), is a crucial devastating rice pest in East Asia. To effectively control this pest, we investigate the genetic diversity, genetic differentiation and genetic structure of 49 populations in China based on a 596 bp fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtDNA <i>COI</i>) gene. Overall, 83 haplotypes were detected in 1253 mtDNA <i>COI</i> sequences. High levels of genetic variability (<i>Hd</i> = 0.756 ± 0.009, <i>π</i> = 0.00416 ± 0.00011) and genetic differentiation (<i>F</i><sub>ST</sub> = 0.262, <i>p</i> < .001) were observed. Bayesian inference phylogenetic and median-joining haplotype network analyses indicated no obvious geographical distribution pattern among haplotypes. Hierarchical AMOVA and SAMOVA revealed no genetically distinct groups and lack of obvious phylogeographic structure. Isolation by distance (IBD) analysis results demonstrated no correlation between genetic differentiation and geographic distance. Finally, the demographic history of SBPH examined by neutrality tests and mismatch distribution analyses illustrated a sudden population expansion at the large spatial scale in China.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"346-354"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1830075","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38465964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Morphology and molecular identification of the zoological origin of medicinal seahorses in Chinese herbal markets.","authors":"Xi Wang, Hongjin Zhong, Jinlin Guo, Feixia Hou","doi":"10.1080/24701394.2020.1815719","DOIUrl":"https://doi.org/10.1080/24701394.2020.1815719","url":null,"abstract":"<p><p>Seahorses are a charismatic group of fish that have high economic value for their unique appearance and important medicinal values. They were heavily traded as traditional Chinese medicines. Authenticating the zoological origin of medicinal seahorses is very difficult because of their similar morphology. To study the identification characteristics of dried seahorse, and to provide a scientific basis for seahorse resource conservation and market supervision, 64 dried specimens from China's four major pharmaceutical markets were investigated based on morphology and COI sequences. Sixty-four COI sequences of 662 bp length revealed 43 unique haplotypes, which were divided into 12 main clades in both NJ and UPGMA phylogenetic trees. Eleven species including <i>Hippocampus spinosissimus</i>, <i>H. barbouri</i>, <i>H. kuda</i>, <i>H. comes</i>, <i>H. histrix</i>, <i>H. trimaculatus</i>, <i>H. kelloggi</i>, <i>H. ingens</i>, <i>H. mohnikei</i>, <i>H. erectus</i> and <i>H. jayakari</i> were clustered on different branches and showed respective monophyly. The results were confirmed by morphology and BLAST analysis. <i>Hippocampus capensis</i> and <i>H. fuscus</i>, which were clustered together in the phylogenetic tree, could be distinguished by different morphology. The morphological and molecular determination revealed 13 seahorse species in Chinese herbal markets. The method of DNA sequences analysis combined with morphological characteristics is conducive to accurately identify the zoological origin of commercial seahorses.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"335-345"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1815719","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38352306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kiran S Kumar, Sivakumar K Chandrika, Sanil George
{"title":"Genetic structure and demographic history of <i>Indirana semipalmata</i>, an endemic frog species of the Western Ghats, India.","authors":"Kiran S Kumar, Sivakumar K Chandrika, Sanil George","doi":"10.1080/24701394.2020.1830077","DOIUrl":"https://doi.org/10.1080/24701394.2020.1830077","url":null,"abstract":"<p><p>The evolutionary potential of a species mainly depends on the level of genetic variation in their populations. Maintenance of gene variation enables populations to adapt more quickly to environmental changes. The geographical gaps also influence the distribution and evolutionary history of many mountain frogs in the world. Hence, a sound knowledge in population genetic structure of a species will help understand its population dynamics and develop conservation strategies. In the context of facing threats to the amphibian fauna of Western Ghats due to habitat loss, we used both mitochondrial and nuclear DNA markers to investigate the genetic structure of an endemic frog species of the Western Ghats (<i>Indirana semipalmata</i>) with restricted distribution. The present study showed the importance of mountain gaps in shaping the species' structuring in the Western Ghats. Though a high genetic diversity was observed for the species when considering a single unit in the southern Western Ghats, the restricted gene flow on/between either side of the Shencottah gap with genetic clustering of the sampled populations may warrant a unique management plan for the species. The habitat fragmentation of the Western Ghats through anthropogenic activities may result in severe setbacks to the survival of the species in the future.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"365-378"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1830077","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38562218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abbas Heydari, Mohammad Ali Oshaghi, Alireza Nazari, Mansoureh Shayeghi, Elham Sanatgar
{"title":"Genetic structure of rice striped stem borer, Chilo suppressalis (Lepidoptera:Crambidae) in North of Iran.","authors":"Abbas Heydari, Mohammad Ali Oshaghi, Alireza Nazari, Mansoureh Shayeghi, Elham Sanatgar","doi":"10.1080/24701394.2020.1815718","DOIUrl":"https://doi.org/10.1080/24701394.2020.1815718","url":null,"abstract":"<p><p>Information on the genetic structure of rice striped stem borer, <i>Chilo suppressalis</i> (Walker), is essential for an effective pest management program and can corporate with control program and prompt the modification of current control methods. In this study, the genetic structure of COI gene has been investigated for 18 populations of this pest in north of Iran. <i>Chilo suppressalis</i> specimens were collected from rice fields on rice and weeds in Guilan and Mazanderan provinces, at Caspian Sea coast at both seasonal activity (spring) and overwintering stage from May through October 2018 and identified using morphological characters. Genetic structure of 18 populations of the species was evaluated using polymerase chain reaction (PCR)-direct-sequencing of a fragment (869 bp) of mtDNA-COI gene. Results revealed that almost all specimens from different generations, hosts, and locations belong to a single haplotype very close to a South Korean haplotype. To the best our knowledge, it is the first comprehensive molecular typing of striped stem borer in both Northern provinces of the country and suggests a high gene flow among different populations of this pest in the region.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"327-334"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1815718","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38440532","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Riazul Islam Barbhuiya, Arif Uddin, Supriyo Chakraborty
{"title":"Codon usage pattern and its influencing factors for mitochondrial <i>CO</i> genes among different classes of Arthropoda.","authors":"Riazul Islam Barbhuiya, Arif Uddin, Supriyo Chakraborty","doi":"10.1080/24701394.2020.1800661","DOIUrl":"https://doi.org/10.1080/24701394.2020.1800661","url":null,"abstract":"<p><p>Analysis of codon usage bias (CUB) is very much important in perceiving the knowledge of molecular biology, the discovery of a new gene, designing of transgenes and evolution of gene. In this study, we analyzed compositional features and codon usage of <i>MT-CO</i> (<i>COI</i>, <i>COII</i> and <i>COIII</i>) genes among the classes of Arthropoda to explore the pattern of CUB as no research work was reported yet. Nucleotide composition analysis in <i>CO</i> genes suggested that the genes were AT-rich in all the four classes of Arthropoda. CUB was low in all the classes of Arthropoda for <i>MT-CO</i> genes as revealed from a high effective number of codons (ENC). We also found that the evolutionary forces namely mutation pressure and natural selection were the key influencing factors in CUB among <i>MT-CO</i> genes as revealed by correlation analysis between overall nucleotide composition and nucleotide composition at the 3rd codon position. Correspondence analysis suggested that the pattern of CUB was different among the classes of Arthropoda. Further, it was revealed from the neutrality plot that natural selection had a dominant role while mutation pressure exhibited a minor role in structuring the pattern of codon usage in all the classes of Arthropoda across <i>COI</i>, <i>COII</i> and <i>COIII</i> genes.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 8","pages":"313-326"},"PeriodicalIF":0.0,"publicationDate":"2020-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1800661","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38239561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Exploring new records of <i>Eutyphoeus</i> sp. (haplotaxida: Octochaetidae) from garo hills, Meghalaya, North Eastern state of India with use of DNA barcodes.","authors":"Samrendra Singh Thakur, Azhar Rashid Lone, Nalini Tiwari, Shweta Yadav","doi":"10.1080/24701394.2020.1781834","DOIUrl":"https://doi.org/10.1080/24701394.2020.1781834","url":null,"abstract":"<p><p>The work was aimed to investigate earthworms species particularly <i>Eutyphoeus</i> endemic to India with the use of DNA barcodes and usual morpho-anatomical standards of earthworm taxonomy from protected areas of Garo Hills, Meghalaya, the north-east region (NER) of India. The study revealed two new records <i>Eutyphoeus kempi</i> Stephenson, <i>E. nepalensis</i> Michaelsen and confirms availability of three known sp. namely <i>E. callosus</i> Gates, <i>E. gammiei</i> Beddard and <i>E. turaensis</i> Stephenson. The neighbor-joining tree was constructed using the K2P substitution model and the genomic signature of each species using <i>COI-1</i> gene was generated for the first time and were used to reconfirm the identification of species.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":"31 7","pages":"265-272"},"PeriodicalIF":0.0,"publicationDate":"2020-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1781834","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38368476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}