Pub Date : 2021-04-01Epub Date: 2021-02-11DOI: 10.1080/24701394.2021.1882444
Nan Song, Qing Zhai, Yaling Zhang
Rove beetles (Staphylinidae) and allied families constitute a huge radiation of Coleoptera, but basal relationships in this group remain controversial. In this study, we newly sequenced eight mitogenomes of representatives of Staphylinidae by using next-generation sequencing method. Together with 99 existing mitogenomes of Staphyliniformia, (sub)family relationships were investigated with ML and Bayesian searches under various substitution models and data recoding schemes. The results consistently supported Scydmaenidae and Silphidae to be subordinate groups of Staphylinidae. Within the monophyletic Staphylinidae (including Scydmaenidae and Silphidae), the hypothesis of four major subfamily groups cannot be confirmed. Bayesian inferences under the site-heterogeneous mixture model generally supported the basal position of major clades corresponding to the Omaliine group. At the subfamily level, the monophyly of Pselaphinae, Oxytelinae, Scaphidiinae, Steninae and Staphylininae was supported. However, the subfamilies Omaliinae, Tachyporinae, Aleocharinae and Paederinae were each non-monophyletic.
{"title":"Higher-level phylogenetic relationships of rove beetles (Coleoptera, Staphylinidae) inferred from mitochondrial genome sequences.","authors":"Nan Song, Qing Zhai, Yaling Zhang","doi":"10.1080/24701394.2021.1882444","DOIUrl":"https://doi.org/10.1080/24701394.2021.1882444","url":null,"abstract":"<p><p>Rove beetles (Staphylinidae) and allied families constitute a huge radiation of Coleoptera, but basal relationships in this group remain controversial. In this study, we newly sequenced eight mitogenomes of representatives of Staphylinidae by using next-generation sequencing method. Together with 99 existing mitogenomes of Staphyliniformia, (sub)family relationships were investigated with ML and Bayesian searches under various substitution models and data recoding schemes. The results consistently supported Scydmaenidae and Silphidae to be subordinate groups of Staphylinidae. Within the monophyletic Staphylinidae (including Scydmaenidae and Silphidae), the hypothesis of four major subfamily groups cannot be confirmed. Bayesian inferences under the site-heterogeneous mixture model generally supported the basal position of major clades corresponding to the Omaliine group. At the subfamily level, the monophyly of Pselaphinae, Oxytelinae, Scaphidiinae, Steninae and Staphylininae was supported. However, the subfamilies Omaliinae, Tachyporinae, Aleocharinae and Paederinae were each non-monophyletic.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1882444","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25356066","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}
Pub Date : 2021-04-01Epub Date: 2021-02-16DOI: 10.1080/24701394.2021.1882443
Megan Whitaker, Taylor Procter, Frank M Fontanella
Dynamic climatic oscillations during the Pleistocene had profound effects on the distribution of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. Analyses of mtDNA sequences from the cytochrome oxidase I gene (911 bp) for 115 individuals of Odontotaenius disjunctus was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. We inferred three lineages that diverged during the Pleistocene and replace each other geographically across the eastern United States. One of these lineages traverses previously identified genetic barriers for terrestrial animals including the Mississippi and Apalachicola Rivers and the Appalachian Mountains. We observed overlapping ranges between two haplotype groups as well as a region of secondary contact associated with ecological transition zone in northern Florida. The two continental lineages depict a genetic signature of a recent population increase associated with expanding niche envelope, whereas the clade restricted to peninsular Florida shows stable populations in a shrinking niche envelope. Given the lack of ecological separation, overlapping distribution of haplogroups and the presence of secondary contact zones, the taxonomic status of these lineages must await robust testing using multilocus DNA data to assess species boundaries.
{"title":"Phylogeography and demographic expansion in the widely distributed horned passalus beetle, <i>Odontotaenius disjunctus</i> (coleoptera: Passalidae).","authors":"Megan Whitaker, Taylor Procter, Frank M Fontanella","doi":"10.1080/24701394.2021.1882443","DOIUrl":"https://doi.org/10.1080/24701394.2021.1882443","url":null,"abstract":"<p><p>Dynamic climatic oscillations during the Pleistocene had profound effects on the distribution of species across North America. Although the role of historical climate change on speciation remains controversial, the impact on genetic variation within species has been well documented. Analyses of mtDNA sequences from the <i>cytochrome oxidase I</i> gene (911 bp) for 115 individuals of <i>Odontotaenius disjunctus</i> was combined with ecological niche modelling (ENM) to infer the demographic and population differentiation scenarios under present and past conditions. We inferred three lineages that diverged during the Pleistocene and replace each other geographically across the eastern United States. One of these lineages traverses previously identified genetic barriers for terrestrial animals including the Mississippi and Apalachicola Rivers and the Appalachian Mountains. We observed overlapping ranges between two haplotype groups as well as a region of secondary contact associated with ecological transition zone in northern Florida. The two continental lineages depict a genetic signature of a recent population increase associated with expanding niche envelope, whereas the clade restricted to peninsular Florida shows stable populations in a shrinking niche envelope. Given the lack of ecological separation, overlapping distribution of haplogroups and the presence of secondary contact zones, the taxonomic status of these lineages must await robust testing using multilocus DNA data to assess species boundaries.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2021.1882443","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25373552","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}
Mutations in mitochondrial DNA (mtDNA) are important causes for type 2 diabetes mellitus (T2DM). To investigate the association between mtDNA mutations/variants and diabetes, we reported here clinical, genetic and biochemical characterization of a Chinese pedigree with maternally transmitted T2DM. Using PCR and direct sequencing analysis of mitochondrial genomes from the matrilineal relatives, we identified two potential pathogenic mutations, m.T4216C (p.Y304H) and m.C5178A (p.L237M) in the ND1 and ND2 genes, respectively, together with a set of genetic polymorphisms belonging to the human mitochondrial haplogroup D4b. Moreover, by isolating and analyzing polymononuclear leukocytes generated from the T2DM patients and controls, we identified lower levels of mitochondrial membrane potential and ATP production in T2DM patients than in the controls, in contrast, a significantly higher level of reactive oxygen species was observed in the T2DM patients carrying both of the m.T4216C and m.C5178A mutations (p < 0.05 for all). In addition, the plasma levels of malondialdehyde and 8-hydroxydeoxyguanosine in the T2DM patients markedly increased, while the level of superoxide dismutase decreased (p < 0.05 for all). Taken together, our data indicated that the ND1 T4216C and ND2 C5178A mutations may lead to oxidative stress and impair the mitochondrial function, and this, in turn, might have been involved in the pathogenesis and progression of T2DM in this pedigree. Thus, our study provides novel insight into the pathophysiology of T2DM that is manifested by mitochondrial dysfunction.
{"title":"Mitochondrial <i>ND1</i> T4216C and <i>ND2</i> C5178A mutations are associated with maternally transmitted diabetes mellitus.","authors":"Zhaochang Jiang, Lili Teng, Shunrong Zhang, Yu Ding","doi":"10.1080/24701394.2020.1856101","DOIUrl":"https://doi.org/10.1080/24701394.2020.1856101","url":null,"abstract":"<p><p>Mutations in mitochondrial DNA (mtDNA) are important causes for type 2 diabetes mellitus (T2DM). To investigate the association between mtDNA mutations/variants and diabetes, we reported here clinical, genetic and biochemical characterization of a Chinese pedigree with maternally transmitted T2DM. Using PCR and direct sequencing analysis of mitochondrial genomes from the matrilineal relatives, we identified two potential pathogenic mutations, m.T4216C (p.Y304H) and m.C5178A (p.L237M) in the <i>ND1</i> and <i>ND2</i> genes, respectively, together with a set of genetic polymorphisms belonging to the human mitochondrial haplogroup D4b. Moreover, by isolating and analyzing polymononuclear leukocytes generated from the T2DM patients and controls, we identified lower levels of mitochondrial membrane potential and ATP production in T2DM patients than in the controls, in contrast, a significantly higher level of reactive oxygen species was observed in the T2DM patients carrying both of the m.T4216C and m.C5178A mutations (<i>p</i> < 0.05 for all). In addition, the plasma levels of malondialdehyde and 8-hydroxydeoxyguanosine in the T2DM patients markedly increased, while the level of superoxide dismutase decreased (<i>p</i> < 0.05 for all). Taken together, our data indicated that the <i>ND1</i> T4216C and <i>ND2</i> C5178A mutations may lead to oxidative stress and impair the mitochondrial function, and this, in turn, might have been involved in the pathogenesis and progression of T2DM in this pedigree. Thus, our study provides novel insight into the pathophysiology of T2DM that is manifested by mitochondrial dysfunction.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1856101","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38680148","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}
Pub Date : 2021-03-01Epub Date: 2021-01-08DOI: 10.1080/24701394.2020.1865940
Dan Wharton, Kevin C Morey, Robert Hanner
This study represents a continuation of a backcrossing experiment initiated in 1982 and reported on earlier after seven generations of backcrossing (Gyllensten et al. 1985) and again after 26 generations (Gyllensten et al. 1991). For the better part of 50 years, it has been demonstrated that mitochondrial DNA (mtDNA) has a largely, if not exclusively maternal mode of inheritance among the multicellular organisms studied to date (Dawid and Blackler 1972; Hutchison et al. 1974; Francisco et al. 1979; Giles et al. 1980; Reilly and Thomas 1980 as cited in Gyllensten et al. 1985). Few studies of invertebrates and no studies of vertebrates have examined maternal inheritance of mtDNA over the course of 139 generations as is the case here (Degrugillier and Newman 1993). Our initial results identify 100% conformity of mtDNA with M. spretus suggesting that any potential paternal contribution of mtDNA to this mouse lineage will require more detailed analysis to detect it.
{"title":"Maternal inheritance of mitochondrial DNA in mice after inter-species hybridization and 138 generations of backcrossing.","authors":"Dan Wharton, Kevin C Morey, Robert Hanner","doi":"10.1080/24701394.2020.1865940","DOIUrl":"https://doi.org/10.1080/24701394.2020.1865940","url":null,"abstract":"This study represents a continuation of a backcrossing experiment initiated in 1982 and reported on earlier after seven generations of backcrossing (Gyllensten et al. 1985) and again after 26 generations (Gyllensten et al. 1991). For the better part of 50 years, it has been demonstrated that mitochondrial DNA (mtDNA) has a largely, if not exclusively maternal mode of inheritance among the multicellular organisms studied to date (Dawid and Blackler 1972; Hutchison et al. 1974; Francisco et al. 1979; Giles et al. 1980; Reilly and Thomas 1980 as cited in Gyllensten et al. 1985). Few studies of invertebrates and no studies of vertebrates have examined maternal inheritance of mtDNA over the course of 139 generations as is the case here (Degrugillier and Newman 1993). Our initial results identify 100% conformity of mtDNA with M. spretus suggesting that any potential paternal contribution of mtDNA to this mouse lineage will require more detailed analysis to detect it.","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1865940","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38795878","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}
Pub Date : 2021-03-01Epub Date: 2021-01-11DOI: 10.1080/24701394.2020.1857198
{"title":"Expression of concern.","authors":"","doi":"10.1080/24701394.2020.1857198","DOIUrl":"https://doi.org/10.1080/24701394.2020.1857198","url":null,"abstract":"","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1857198","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38806561","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}
Morphological identification of the commonest Indian freshwater calanoid copepod Heliodiaptomus viduus has been facing a lot of controversies. To solve this problem, additional molecular support is needed. Hence, molecular analysis, along with morphological identification of the species using scanning electron microscopy (SEM) and optical microscopy, was carried out. The genetic distance between the intraspecific sequences in the 18SrRNA observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.002. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic trees with 100% bootstrap value. The genetic distance between the intraspecific sequences in the mtCOI observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.267 and lay in a separate clade in the phylogenetic tree from the within genus clade. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic tree with above 75% bootstrap value. Hence, the 18S rRNA (MH145356, MK457456) and mtCOI (MK621900) gene sequences of the present study are well supported the identification of H. viduus and it serves as the first molecular database besides providing morphological authentication (SEM images) of H.viduus. This combined analysis is envisioned to be helpful in selecting the ecologically and nutritionally important species for practical aquaculture.
{"title":"Morphological and molecular analysis of the freshwater copepod <i>Heliodiaptomus viduus</i> (Calanoida: Diaptomidae).","authors":"Mayavan Karthika, Shameem Shabana, Venkatachalam Ramasubramanian","doi":"10.1080/24701394.2020.1845324","DOIUrl":"https://doi.org/10.1080/24701394.2020.1845324","url":null,"abstract":"<p><p>Morphological identification of the commonest Indian freshwater calanoid copepod <i>Heliodiaptomus viduus</i> has been facing a lot of controversies. To solve this problem, additional molecular support is needed. Hence, molecular analysis, along with morphological identification of the species using scanning electron microscopy (SEM) and optical microscopy, was carried out. The genetic distance between the intraspecific sequences in the 18SrRNA observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.002. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic trees with 100% bootstrap value. The genetic distance between the intraspecific sequences in the mtCOI observed to be 0.000, while the interspecific distance within genus sequences varied from 0.000 to 0.267 and lay in a separate clade in the phylogenetic tree from the within genus clade. Besides, it was noted that both the sequences (intraspecific) were present within a single clade of the phylogenetic tree with above 75% bootstrap value. Hence, the 18S rRNA (MH145356, MK457456) and mtCOI (MK621900) gene sequences of the present study are well supported the identification of <i>H. viduus</i> and it serves as the first molecular database besides providing morphological authentication (SEM images) of <i>H.viduus</i>. This combined analysis is envisioned to be helpful in selecting the ecologically and nutritionally important species for practical aquaculture.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1845324","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38594351","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}
Pub Date : 2021-03-01Epub Date: 2020-12-11DOI: 10.1080/24701394.2020.1856828
Ang Li, Zhe Hou
The distribution pattern and genetic structure of plant species have been profoundly influenced by climate oscillations. Phylogeographic analyses have been numerously conducted in biodiversity hotspot regions and some general conclusions have been documented. However, other regions have received less attentions and these places may serve as potential glacial refugia for plant species to survive the Quaternary glaciation. Here, we used six nuclear and three cpDNA markers to estimate the phylogeographic pattern of Populus davidiana, a widespread species distributed in southwest China. As a widely distributed species in southwest China, the nucleotide diversity of P. davidiana was relatively high (Na = 6.28, HO = 0.534, and HE = 0.658). Genetic differentiation (FST) between the two main distribution regions, Yunnan and Guizhou provinces, was 0.21221. According to the composition of chloroplast haplotypes and the result of structure in these populations, we clearly distinguished two distantly sublineages corresponding to two distribution regions. Results of the Mantel test showed that there was a significant correlation between genetic distance and geographical distance (R2 = 0.8252, p<.05). The topographically heterogeneous regions and the low dispersal ability of seed and pollen may lead to high genetic differentiation between these two regions. A potential glacial refugia for P. davidiana located in adjacent regions to the Hengduan range was revealed and allopatric divergence in separated glacial refugia may directly lead to the present phylogeographic pattern of this species.
植物物种的分布格局和遗传结构受到气候变化的深刻影响。在生物多样性热点地区进行了大量的系统地理学分析,并得出了一些一般性的结论。然而,其他地区受到的关注较少,这些地方可能是第四纪冰川时期植物物种生存的潜在冰川避难所。本文利用6个核标记和3个cpDNA标记对中国西南地区分布广泛的大杨树(Populus davidiana)的系统地理格局进行了分析。作为西南地区分布较广的一种,大花草核苷酸多样性较高(Na = 6.28, HO = 0.534, HE = 0.658)。云南和贵州两个主要分布区的遗传分化(FST)为0.21221。根据这些居群的叶绿体单倍型组成和结构结果,我们明确区分了两个远缘亚系,对应于两个分布区域。Mantel检验结果表明,遗传距离与地理距离之间存在显著的相关关系(R2 = 0.8252),揭示了横断山脉相邻地区的大戟属植物,分离的冰川避难区内的异域分化可能直接导致了该物种目前的系统地理格局。
{"title":"Phylogeographic analyses of poplar revealed potential glacial refugia and allopatric divergence in southwest China.","authors":"Ang Li, Zhe Hou","doi":"10.1080/24701394.2020.1856828","DOIUrl":"https://doi.org/10.1080/24701394.2020.1856828","url":null,"abstract":"<p><p>The distribution pattern and genetic structure of plant species have been profoundly influenced by climate oscillations. Phylogeographic analyses have been numerously conducted in biodiversity hotspot regions and some general conclusions have been documented. However, other regions have received less attentions and these places may serve as potential glacial refugia for plant species to survive the Quaternary glaciation. Here, we used six nuclear and three cpDNA markers to estimate the phylogeographic pattern of <i>Populus davidiana</i>, a widespread species distributed in southwest China. As a widely distributed species in southwest China, the nucleotide diversity of <i>P. davidiana</i> was relatively high (<i>N</i><sub>a</sub> = 6.28, <i>H</i><sub>O</sub> = 0.534, and <i>H</i><sub>E</sub> = 0.658). Genetic differentiation (<i>F</i><sub>ST</sub>) between the two main distribution regions, Yunnan and Guizhou provinces, was 0.21221. According to the composition of chloroplast haplotypes and the result of structure in these populations, we clearly distinguished two distantly sublineages corresponding to two distribution regions. Results of the Mantel test showed that there was a significant correlation between genetic distance and geographical distance (<i>R</i><sup>2</sup> = 0.8252, <i>p</i><.05). The topographically heterogeneous regions and the low dispersal ability of seed and pollen may lead to high genetic differentiation between these two regions. A potential glacial refugia for <i>P. davidiana</i> located in adjacent regions to the Hengduan range was revealed and allopatric divergence in separated glacial refugia may directly lead to the present phylogeographic pattern of this species.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1856828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38698890","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}
Mitochondrial DNA cytochrome b and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby Rhinogobius delicatus from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation (FST=0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of R. delicatus were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, Onychostoma alticorpus, Aphyocypris kikuckii and Hemimyzon taitungensis, our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.
{"title":"Genetic diversity of <i>Rhinogobius delicatus</i> (Perciformes: Gobiidae): origins of the freshwater fish in East Taiwan.","authors":"Yu-Min Ju, Jui-Hsien Wu, Kui-Ching Hsu, Yu-Wen Chiu, Wei-Kuang Wang, Chih-Wei Chen, Hung-Du Lin","doi":"10.1080/24701394.2020.1844678","DOIUrl":"https://doi.org/10.1080/24701394.2020.1844678","url":null,"abstract":"<p><p>Mitochondrial DNA cytochrome <i>b</i> and d-loop sequences (1,984 bp) from 92 specimens of the freshwater goby <i>Rhinogobius delicatus</i> from seven drainages in East Taiwan were identified as two major lineages exhibiting a southern or northern distribution. The existence of low genetic diversity, a pattern of population decline and high population differentiation (<i>F</i><sub>ST</sub>=0.711) support the need for the development of management strategies for the conservation of localized populations. The results of a statistical dispersal-vicariance analysis suggested that the ancestral populations of <i>R. delicatus</i> were widely distributed in East Taiwan. Compared with the phylogeographic patterns of the other endemic eastern Taiwan freshwater fishes, <i>Onychostoma alticorpus</i>, <i>Aphyocypris kikuckii</i> and <i>Hemimyzon taitungensis</i>, our study suggests that the freshwater fishes colonized East Taiwan through northeastern and southwestern Taiwan, although the ancestral populations colonized the island before it reached its present shape.</p>","PeriodicalId":74204,"journal":{"name":"Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/24701394.2020.1844678","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38592601","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}
Pub Date : 2021-01-01Epub Date: 2020-12-21DOI: 10.1080/24701394.2020.1844679
Maira A Rizo-Fuentes, Camilo A Correa-Cárdenas, Carlos A Lasso, Mónica A Morales-Betancourt, Dalia C Barragán-Barrera, Susana Caballero
The freshwater stingray Paratrygon aiereba 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 P. aiereba distributed in the Amazon and Orinoco basins, we amplified Cytochrome oxidase subunit 1 (COI) partial region of mitochondrial DNA (mtDNA) in 50 samples from eight different sub-basins. Our results suggest three phylogroups and a vicariance event occurred 43 million years ago proposing how Paratrygon diverged into the basins. A high population structure (ΦST = 0.692; p < 0.005) and a value of (K) of 3 were defined. A high genetic diversity within phylogroups was found: Phylogroup A (h = 0.64; π% = 2.48), Phylogroup B (h = 0.552; π% = 1.67), and Phylogroup C (h = 0.49; π% = 0.73). These results should be considered in local management plans, conservation programs and reclassification in at least Amazon and Orinoco.
{"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":null,"pages":null},"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}
Pub Date : 2021-01-01Epub Date: 2020-11-09DOI: 10.1080/24701394.2020.1844677
Gabriel Iketani, Luciana Pimentel, Ezequias Dos Santos Torres, Péricles Sena do Rêgo, Iracilda Sampaio
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 Macrobrachium amazonicum, 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 M. amazonicum populations, and we recommend caution when using COI for genetic inferences in prawns of the genus Macrobrachium, and in particular that any analysis should include nuclear markers.
{"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":null,"pages":null},"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}