Genetica最新文献_第8页

The signals of selective constraints on the mitochondrial non-coding control region: insights from comparative mitogenomics of Clupeoid fishes. 线粒体非编码控制区的选择性约束信号:来自棍棒类鱼类比较线粒体基因组学的见解。

IF 1.5 4区生物学

Genetica Pub Date : 2021-06-01 Epub Date: 2021-04-29 DOI: 10.1007/s10709-021-00121-x

Wilson Sebastian, Sandhya Sukumaran, A Gopalakrishnan

{"title":"The signals of selective constraints on the mitochondrial non-coding control region: insights from comparative mitogenomics of Clupeoid fishes.","authors":"Wilson Sebastian, Sandhya Sukumaran, A Gopalakrishnan","doi":"10.1007/s10709-021-00121-x","DOIUrl":"https://doi.org/10.1007/s10709-021-00121-x","url":null,"abstract":"The vertebrate mitochondrial genome is characterized by an exceptional organization evolving towards a reduced size. However, the persistence of a non-coding and highly variable control region is against this evolutionary trend that is explained by the presence of conserved sequence motifs or binding sites for nuclear-organized proteins that regulate mtDNA maintenance and expression. We performed a comparative mitogenomic investigation of the non-coding control region to understand its evolutionary patterns in Clupeoid fishes which are widely distributed across oceans of the world, exhibiting exemplary evolutionary potential. We confirmed the ability of sequence flanking the conserved sequence motifs in the control region to form stable secondary structures. The existence of evolutionarily conserved secondary structures without primary structure conservation suggested the action of selective constraints towards maintaining the secondary structure. The functional secondary structure is maintained by retaining the frequency of discontinuous AT and TG repeats along with compensatory base substitutions in the stem forming regions which can be considered as a selective constraint. The nucleotide polymorphism along the flanking regions of conserved sequence motifs can be explained as errors during the enzymatic replication of secondary structure-forming repeat elements. The evidence for selective constraints on secondary structures emphasizes the role of the control region in mitogenome function. Maintenance of high frequency of discontinuous repeats can be proposed as a model of adaptive evolution against the mutations that break the secondary structure involved in the efficient regulation of mtDNA functions substantiating the efficient functioning of the control region even in a high nucleotide polymorphism environment.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-021-00121-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38920774","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}

引用次数: 1

Fine-scale genetic structure of the endangered bitterling in the middle river basin of the Kiso River, Japan. 日本木索河中河流域濒危苦鱼的精细遗传结构。

IF 1.5 4区生物学

Genetica Pub Date : 2021-06-01 Epub Date: 2021-05-02 DOI: 10.1007/s10709-021-00123-9

Yuji Yamazaki, Jyun-Ichi Kitamura, Koki Ikeya, Seiichi Mori

{"title":"Fine-scale genetic structure of the endangered bitterling in the middle river basin of the Kiso River, Japan.","authors":"Yuji Yamazaki, Jyun-Ichi Kitamura, Koki Ikeya, Seiichi Mori","doi":"10.1007/s10709-021-00123-9","DOIUrl":"https://doi.org/10.1007/s10709-021-00123-9","url":null,"abstract":"Recently, anthropogenic alterations have had severe and negative impacts on the terrestrial and aquatic species and environments. To conserve species that have a small and limited habitat, it is necessary to focus on fine-scale population structure and its effects on persistence. The deepbodied bitterling Acheilognathus longipinnis is an endangered freshwater fish that occupies ponds scattered in lateral bars in the Kiso River. In this study, we conducted multi-locus microsatellite DNA analysis to evaluate both fine-scale population structure and genetic diversity, in order to conserve A. longipinnis. The smaller number of loci deviating from the Hardy-Weinberg equilibrium in ponds scattered in individual lateral bars compared to the whole river system suggests that A. longipinnis forms a local breeding population in units of ponds. The population was roughly split between the river banks and the local population located in ponds in the mid-channel bar showed intermediate relationships with the river bank populations. Gene flow between local populations was not always homogeneous and was not influenced by geographical distances between local populations or the direction of river flow. The dispersal of A. longipinnis across both river bank sides may be constrained and is probably affected by the ecological characteristics of A. longipinnis and the hydrological regimes. Consequently, A. longipinnis in the Kiso River is maintained as a complex of multiple local populations with appropriate gene flow among them. To conserve A. longipinnis, both the persistence of the unstable ponds and moderate genetic exchanges by individual migration are required.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-021-00123-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38948338","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}

引用次数: 5

False and true positives in arthropod thermal adaptation candidate gene lists. 节肢动物热适应候选基因表的假阳性和真阳性。

IF 1.5 4区生物学

Genetica Pub Date : 2021-06-01 Epub Date: 2021-05-07 DOI: 10.1007/s10709-021-00122-w

Maike Herrmann, Lev Y Yampolsky

{"title":"False and true positives in arthropod thermal adaptation candidate gene lists.","authors":"Maike Herrmann, Lev Y Yampolsky","doi":"10.1007/s10709-021-00122-w","DOIUrl":"https://doi.org/10.1007/s10709-021-00122-w","url":null,"abstract":"Genome-wide studies are prone to false positives due to inherently low priors and statistical power. One approach to ameliorate this problem is to seek validation of reported candidate genes across independent studies: genes with repeatedly discovered effects are less likely to be false positives. Inversely, genes reported only as many times as expected by chance alone, while possibly representing novel discoveries, are also more likely to be false positives. We show that, across over 30 genome-wide studies that reported Drosophila and Daphnia genes with possible roles in thermal adaptation, the combined lists of candidate genes and orthologous groups are rapidly approaching the total number of genes and orthologous groups in the respective genomes. This is consistent with the expectation of high frequency of false positives. The majority of these spurious candidates have been identified by one or a few studies, as expected by chance alone. In contrast, a noticeable minority of genes have been identified by numerous studies with the probabilities of such discoveries occurring by chance alone being exceedingly small. For this subset of genes, different studies are in agreement with each other despite differences in the ecological settings, genomic tools and methodology, and reporting thresholds. We provide a reference set of presumed true positives among Drosophila candidate genes and orthologous groups involved in response to changes in temperature, suitable for cross-validation purposes. Despite this approach being prone to false negatives, this list of presumed true positives includes several hundred genes, consistent with the \"omnigenic\" concept of genetic architecture of complex traits.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-021-00122-w","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38971623","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}

引用次数: 6

Neutralism versus selectionism: Chargaff's second parity rule, revisited. 中立主义与选择主义:重新审视Chargaff的第二宇称规则。

IF 1.5 4区生物学

Genetica Pub Date : 2021-04-01 Epub Date: 2021-04-20 DOI: 10.1007/s10709-021-00119-5

Donald R Forsdyke

{"title":"Neutralism versus selectionism: Chargaff's second parity rule, revisited.","authors":"Donald R Forsdyke","doi":"10.1007/s10709-021-00119-5","DOIUrl":"https://doi.org/10.1007/s10709-021-00119-5","url":null,"abstract":"Of Chargaff's four \"rules\" on DNA base frequencies, the functional interpretation of his second parity rule (PR2) is the most contentious. Thermophile base compositions (GC%) were taken by Galtier and Lobry (1997) as favoring Sueoka's neutral PR2 hypothesis over Forsdyke's selective PR2 hypothesis, namely that mutations improving local within-species recombination efficiency had generated a genome-wide potential for the strands of duplex DNA to separate and initiate recombination through the \"kissing\" of the tips of stem-loops. However, following Chargaff's GC rule, base composition mainly reflects a species-specific, genome-wide, evolutionary pressure. GC% could not have consistently followed the dictates of temperature, since it plays fundamental roles in both sustaining species integrity and, through primarily neutral genome-wide mutation, fostering speciation. Evidence for a local within-species recombination-initiating role of base order was obtained with a novel technology that masked the contribution of base composition to nucleic acid folding energy. Forsdyke's results were consistent with his PR2 hypothesis, appeared to resolve some root problems in biology and provided a theoretical underpinning for alignment-free taxonomic analyses using relative oligonucleotide frequencies (k-mer analysis). Moreover, consistent with Chargaff's cluster rule, discovery of the thermoadaptive role of the \"purine-loading\" of open reading frames made less tenable the Galtier-Lobry anti-selectionist arguments.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-021-00119-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38893934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

The use of an integrative approach to improve accuracy of species identification and detection of new species in studies of stream fish diversity. 在溪流鱼类多样性研究中，利用综合方法提高物种鉴定和新物种发现的准确性。

IF 1.5 4区生物学

Genetica Pub Date : 2021-04-01 Epub Date: 2021-04-20 DOI: 10.1007/s10709-021-00118-6

Luiz Henrique Garcia Pereira, Jerson Rogelio Chanchay Castro, Pilar Mireya Huatatoca Vargas, Jose Alejandro Morales Gomez, Claudio Oliveira

{"title":"The use of an integrative approach to improve accuracy of species identification and detection of new species in studies of stream fish diversity.","authors":"Luiz Henrique Garcia Pereira, Jerson Rogelio Chanchay Castro, Pilar Mireya Huatatoca Vargas, Jose Alejandro Morales Gomez, Claudio Oliveira","doi":"10.1007/s10709-021-00118-6","DOIUrl":"https://doi.org/10.1007/s10709-021-00118-6","url":null,"abstract":"In this study, we made an inventory of the stream and headwater ichthyofauna of the left bank of the Itaipu Dam Reservoir, located in the lower part of the Upper Paraná River basin, using an integrative approach of molecular and morphological data. The area is located in the western portion of the Paraná state in Brazil, in an area of about 8,000 km2 highly impacted by deforestation and intensive agriculture. For taxonomic identification of species, we used an identification key combined with the DNA barcoding approach. We found 48 species belonging to six orders, 13 families, and 37 genera. The Siluriformes and Characiformes were the most representative orders (75%) and the Characidae was the most representative family (20.8%). Nine species prevailed in this region, making up to 86% of all specimens collected. The integrative approach proved to be useful by allowing the unambiguous identification of all species, including those cases in which morphological characters were not conclusive for species identification, cases of cryptic species, and species with high morphological plasticity. In addition, the integrative approach highlighted six to 13 new putative species depending on the approach considered. Our study provides a relevant contribution to the knowledge of fish diversity in a poorly studied area of the Paraná River basin. We showed that the use of an integrative approach in inventory studies improves species identification and the discovery of new, cryptic, and overlooked species, being a powerful and necessary tool to quantify biodiversity.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-021-00118-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38892268","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}

引用次数: 10

Intraspecific genetic variation for anesthesia success in a New Zealand freshwater snail. 新西兰淡水蜗牛麻醉成功的种内遗传变异。

IF 1.5 4区生物学

Genetica Pub Date : 2021-02-01 Epub Date: 2021-01-03 DOI: 10.1007/s10709-020-00110-6

Qiudong Song, Richard Magnuson, Joseph Jalinsky, Marissa Roseman, Maurine Neiman

引用次数: 1

Molecular cloning and transcriptional regulation of two γ-carbonic anhydrase genes in the green macroalga Ulva prolifera. 绿藻两个γ-碳酸酐酶基因的克隆及转录调控。

IF 1.5 4区生物学

Genetica Pub Date : 2021-02-01 Epub Date: 2021-01-15 DOI: 10.1007/s10709-020-00112-4

Yu Wang, Feng Liu, Manman Liu, Shitao Shi, Yuping Bi, Nansheng Chen

{"title":"Molecular cloning and transcriptional regulation of two γ-carbonic anhydrase genes in the green macroalga Ulva prolifera.","authors":"Yu Wang, Feng Liu, Manman Liu, Shitao Shi, Yuping Bi, Nansheng Chen","doi":"10.1007/s10709-020-00112-4","DOIUrl":"https://doi.org/10.1007/s10709-020-00112-4","url":null,"abstract":"Ulva prolifera O.F. Müller (Ulvophyceae, Chlorophyta) is well known as a typical green-tide forming macroalga which has caused the world's largest macroalgal blooms in the Yellow Sea of China. In this study, two full-length γ-carbonic anhydrase (γ-CA) genes (UpγCA1 and UpγCA2) were cloned from U. prolifera. UpγCA1 has three conserved histidine residues, which act as an active site for binding a zinc metal ion. In UpγCA2, two of the three histidine residues were replaced by serine and arginine, respectively. The two γ-CA genes are clustered together with other γ-CAs in Chlorophyta with strong support value (100% bootstrap) in maximum likelihood (ML) phylogenetic tree. Quantitative real-time PCR (qRT-PCR) analysis showed that stressful environmental conditions markedly inhibited transcription levels of these two γ-CA genes. Low pH value (pH 7.5) significantly increased transcription level of UpγCA2 not UpγCA1 at 12 h, whereas high pH value (pH 8.5) significantly inhibited the transcription of these two γ-CA genes at 6 h. These findings enhanced our understanding on transcriptional regulation of γ-CA genes in response to environmental factors in U. prolifera.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-020-00112-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38756601","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}

引用次数: 1

Population genetic structure of the highly endangered butterfly Coenonympha oedippus (Nymphalidae: Satyrinae) at its southern edge of distribution. 高度濒危蝴蝶oedippus Coenonympha oedippus(蛱蝶科:蛱蝶科)分布南缘种群遗传结构。

IF 1.5 4区生物学

Genetica Pub Date : 2021-02-01 Epub Date: 2021-01-03 DOI: 10.1007/s10709-020-00108-0

Sara Zupan, Jure Jugovic, Tatjana Čelik, Elena Buzan

{"title":"Population genetic structure of the highly endangered butterfly Coenonympha oedippus (Nymphalidae: Satyrinae) at its southern edge of distribution.","authors":"Sara Zupan, Jure Jugovic, Tatjana Čelik, Elena Buzan","doi":"10.1007/s10709-020-00108-0","DOIUrl":"https://doi.org/10.1007/s10709-020-00108-0","url":null,"abstract":"The Slovenian False Ringlet Coenonympha oedippus populations are under serious threat, as in the last two decades have witnessed a sharp decline in population distribution and size due to destruction, fragmentation and/or habitat quality degradation through intensive agriculture, abandonment of use and urbanization. We investigated the genetic diversity and structure of C. oedippus from the entire range of the species in Slovenia. Our results showed that the genetic variation in the Slovenian C. oedippus populations agrees with the geographical structure and the ecotypes previously determined by morphological and ecological data. We confirmed the existence of four genetically divergent and spatially non-overlapping geographical groups (Istria, Karst, Gorica, Ljubljansko barje) and two ecotypes (\"wet\" and \"dry\"). Despite small sample sizes due to critically threatened species, the results indicated significant nuclear and mitochondrial genetic diversity within the spatial groups. By gaining new insights into the evolutionary history of the C. oedippus population, we have recommended to consider the Slovenian population as one Evolutionary Significant Unit, and four spatial populations as Management Units for conservation purposes.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-020-00108-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38774554","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}

引用次数: 0

Streptomycin and nalidixic acid elevate the spontaneous genome-wide mutation rate in Escherichia coli. 链霉素和萘啶酸可提高大肠杆菌的自发全基因组突变率。

IF 1.5 4区生物学

Genetica Pub Date : 2021-02-01 Epub Date: 2021-01-27 DOI: 10.1007/s10709-021-00114-w

Huseyin Ozgur Ozdemirel, Dilara Ulusal, Sibel Kucukyildirim Celik

引用次数: 5

Molecular cytogenetics in the study of repetitive sequences helping to understand the evolution of heterochromatin in Melipona (Hymenoptera, Meliponini). 重复序列的分子细胞遗传学研究有助于了解蜂属异染色质的进化。

IF 1.5 4区生物学

Genetica Pub Date : 2021-02-01 Epub Date: 2021-01-15 DOI: 10.1007/s10709-020-00111-5

Jaqueline Amorim Pereira, Natália Martins Travenzoli, Monique Póvoa de Oliveira, Hugo de Azevedo Werneck, Tânia Maria Fernandes Salomão, Denilce Meneses Lopes

{"title":"Molecular cytogenetics in the study of repetitive sequences helping to understand the evolution of heterochromatin in Melipona (Hymenoptera, Meliponini).","authors":"Jaqueline Amorim Pereira, Natália Martins Travenzoli, Monique Póvoa de Oliveira, Hugo de Azevedo Werneck, Tânia Maria Fernandes Salomão, Denilce Meneses Lopes","doi":"10.1007/s10709-020-00111-5","DOIUrl":"https://doi.org/10.1007/s10709-020-00111-5","url":null,"abstract":"The eukaryote genome is enriched by different types of repetitive DNA sequences and is most abundant in heterochromatin regions. Historically, no function has been assigned to these sequences, which makes them the target of studies that have demonstrated their structural and functional importance in the genome. Despite having a constant chromosome number, the genus Melipona has species with wide variation in heterochromatin content, from 8 to 73%, which is an important feature to be investigated regarding its origin and evolution. In the present study, a repetitive DNA sequence of Melipona mondury was isolated by restriction enzyme digestion. This sequence was used to hybridize chromosomes of eight Melipona species that include representatives of the four subgenera and present divergent characteristics in relation to the heterochromatin content. Considering that rDNA localization has shown differences in Melipona, 16 species of this genus were analyzed with 18S rDNA probe. Our data suggest that heterochromatin growth occurred independently in the Michmelia and Melikerria subgenera, considering that the isolated repetitive DNA sequence was shared only by the Michmelia species. Amplification possibly occurred from the centromeric region, causing the displacement of the rDNA sites to the ends of the chromosomes. The repetitive DNA sequence used is a constituent of Michmelia heterochromatin, which that arose from the common ancestor of the species of this subgenus.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":null,"pages":null},"PeriodicalIF":1.5,"publicationDate":"2021-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-020-00111-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38756600","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}

引用次数: 10