scholarly journals Complete paternally inherited mitogenomes of two freshwater mussels Unio pictorum and Sinanodonta woodiana (Bivalvia: Unionidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5573 ◽  
Author(s):  
Artur Burzyński ◽  
Marianna Soroka
Keyword(s):  
Evolutionary Dynamics ◽  
Phylogenetic Reconstruction ◽  
Real Problem ◽  
Data Sets ◽  
Long Branch Attraction ◽  
The Family ◽  
Complete Sequences ◽  
First Time ◽  
Unio Pictorum ◽  
Sinanodonta Woodiana

Freshwater bivalves from the family Unionidae usually have two very divergent mitogenomes, inherited according to the doubly uniparental model. The early divergence of these two mitogenomic lineages gives a unique opportunity to use two mitogenomic data sets in a single phylogenetic context. However, the number of complete sequences of the maternally inherited mitogenomes of these animals available in GenBank greatly exceeds that of the paternally inherited mitogenomes. This is a problem for phylogenetic reconstruction because it limits the use of both mitogenomic data sets. Moreover, since long branch attraction phenomenon can bias reconstructions if only a few but highly divergent taxa are considered, the shortage of the faster evolving paternally inherited mitogenome sequences is a real problem. Here we provide, for the first time, complete sequences of the M mitogenomes sampled from Polish populations of two species: native Unio pictorum and invasive Sinanodonta woodiana. It increases the available set of mitogenomic pairs to 18 species per family, and allows unambiguous reconstruction of phylogenetic relationships among them. The reconstructions based on M and F mitogenomes which were separated for many millions of years, and subject to differing evolutionary dynamics, are fully congruent.

scholarly journals Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda

2019 ◽  
Vol 11 (7) ◽  
pp. 1797-1812 ◽  
Author(s):  
Dong Zhang ◽  
Hong Zou ◽  
Cong-Jie Hua ◽  
Wen-Xiang Li ◽  
Shahid Mahboob ◽  
...  
Keyword(s):  
Life Histories ◽  
Phylogenetic Reconstruction ◽  
Mitochondrial Genomes ◽  
Data Sets ◽  
Long Branch Attraction ◽  
Mitochondrial Data ◽  
Gc Skew ◽  
Limited Applicability ◽  
Phylogenetic Hypotheses ◽  
Almost All

Abstract The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.

Larval Sphindidae (Coleoptera : Cucujoidea): phylogenetic implications and new descriptions

2000 ◽  
Vol 14 (6) ◽  
pp. 807 ◽  
Author(s):  
Erica Chiao ◽  
Joseph V. McHugh
Keyword(s):  
Cladistic Analysis ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Data Sets ◽  
Strong Impact ◽  
Length Difference ◽  
Phylogenetic Implications ◽  
The Family ◽  
Cladistic Analyses ◽  
First Time

A new phylogenetic hypothesis of Sphindidae (Coleoptera: Cucujoidea) ispresented, based on a cladistic analysis of 15 larval morphology characters inaddition to 39 adult morphology characters modified from a previous study by McHugh (1993). Results from the combined cladistic analyses show larval characters supporting several previously established relationships and resolving the placement of Notosphindus McHugh & Wheeler. The sister-group relationship betweenCarinisphindus McHugh and SphindusMegerle in Dejean is not supported by the combined analyses. Larval charactersdid not show a disproportionately strong impact on the more basal nodes.Incongruence length difference analysis found an insignificant level ofdiscordance (P = 0.197) between the adult andlarval based data sets. Larval Notosphindus slateriMcHugh & Wheeler, Genisphindus minor McHugh andCarinisphindus purpuricephalus McHugh & Lewis aredescribed for the first time, representing the first larval descriptions forthese genera. A literature review of immature stages of sphindid beetles and ageneric level key to larvae of the family are provided.

scholarly journals Mitochondrial Genomes, Phylogenetic Associations, and SNP Recovery for the Key Invasive Ponto-Caspian Amphipods in Europe

2021 ◽  
Vol 22 (19) ◽  
pp. 10300
Author(s):  
Tomasz Mamos ◽  
Michał Grabowski ◽  
Tomasz Rewicz ◽  
Jamie Bojko ◽  
Dominik Strapagiel ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Freshwater Ecosystems ◽  
Phylogeny Reconstruction ◽  
Mitochondrial Genomes ◽  
Identification Methods ◽  
Snp Calling ◽  
Genomic Knowledge ◽  
The Family ◽  
Invasive Amphipods ◽  
First Time

The Ponto-Caspian region is the main donor of invasive amphipods to freshwater ecosystems, with at least 13 species successfully established in European inland waters. Dikerogammarus spp. and Pontogammarus robustoides are among the most successful, due to their strong invasive impact on local biota. However, genomic knowledge about these invaders is scarce, while phylogeography and population genetics have been based on short fragments of mitochondrial markers or nuclear microsatellites. In this study, we provide: (i) a reconstruction of six mitogenomes for four invasive gammarids (D. villosus, D. haemobaphes, D. bispinosus, and P. robustoides); (ii) a comparison between the structure of the newly obtained mitogenomes and those from the literature; (iii) SNP calling rates for individual D. villosus and D. haemobaphes from different invasion sites across Europe; and (iv) the first time-calibrated full mitogenome phylogeny reconstruction of several Ponto-Caspian taxa. We found that, in comparison to other gammarids, the mitogenomes of Ponto-Caspian species show a translocation between the tRNA-E and tRNA-R positions. Phylogenetic reconstruction using the mitogenomes identified that Ponto-Caspian gammarids form a well-supported group that originated in the Miocene. Our study supports paraphyly in the family Gammaridae. These provided mitogenomes will serve as vital genetic resources for the development of new markers for PCR-based identification methods and demographic studies.

scholarly journals Complete Sequences of Four Plasmids of Lactococcus lactis subsp. cremoris SK11 Reveal Extensive Adaptation to the Dairy Environment

2005 ◽  
Vol 71 (12) ◽  
pp. 8371-8382 ◽  
Author(s):  
Roland J. Siezen ◽  
Bernadet Renckens ◽  
Iris van Swam ◽  
Sander Peters ◽  
Richard van Kranenburg ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Atp Synthesis ◽  
The Family ◽  
Folate Biosynthesis ◽  
Sequence Elements ◽  
Complete Sequences ◽  
Lactose Utilization ◽  
Oligopeptide Permease ◽  
Electron Sink ◽  
First Time

ABSTRACT Lactococcus lactis strains are known to carry plasmids encoding industrially important traits. L. lactis subsp. cremoris SK11 is widely used by the dairy industry in cheese making. Its complete plasmid complement was sequenced and found to contain the plasmids pSK11A (10,372 bp), pSK11B (13,332 bp), pSK11L (47,165 bp), and pSK11P (75,814 bp). Six highly homologous repB-containing replicons were found, all belonging to the family of lactococcal theta-type replicons. Twenty-three complete insertion sequence elements segment the plasmids into numerous modules, many of which can be identified as functional units or containing functionally related genes. Plasmid-encoded functions previously known to reside on L. lactis SK11 plasmids were now mapped in detail, e.g., lactose utilization (lacR-lacABCDFEGX), the proteolytic system (prtM-prtP, pepO, pepF), and the oligopeptide permease system (oppDFBCA). Newly identified plasmid-encoded functions could facilitate the uptake of various cations, while the pabA and pabB genes could be essential for folate biosynthesis. A competitive advantage could be obtained by using the putative flavin adenine dinucleotide-dependent d-lactate dehydrogenase and oxalate:formate antiporter for enhanced ATP synthesis, while the activity of the predicted α-acetolactate decarboxylase may contribute to the formation of an additional electron sink. Various stress response proteins are plasmid encoded, which could enhance strain robustness. A substantial number of these “adaptation” genes have not been described before on L. lactis plasmids. Moreover, several genes were identified for the first time in L. lactis, possibly reflecting horizontal gene transfer.

scholarly journals Sequence diversity and evolution of a group of iflaviruses associated with ticks

2021 ◽  
Author(s):  
Romain Daveu ◽  
Caroline Hervet ◽  
Louane Sigrist ◽  
Davide Sassera ◽  
Aaron Jex ◽  
...  
Keyword(s):  
Cell Line ◽  
Evolutionary Dynamics ◽  
Ixodes Scapularis ◽  
Data Sets ◽  
Virus Species ◽  
Rna Seq ◽  
Genome Sequences ◽  
Synonymous Mutations ◽  
The Family ◽  
Insight Into

AbstractWe studied a group of tick-associated viruses with characteristics of members of the family Iflaviridae, a family of viruses frequently found in arthropods. Our aim was to gain insight into the evolutionary dynamics of this group of viruses, which may be linked to the biology of ticks. We explored assembled RNA-Seq data sets for different species of ticks. We identified members of five different iflavirus species, four of them novel, and discovered nine new genome sequences, including variants. Five variants represented a virus species associated with Ixodes ricinus. Unexpectedly, a sequence found in the Ixodes scapularis cell line ISE6 was nearly identical to the sequences of I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Analysing patterns of substitutions between these variants, we detected a strong excess of synonymous mutations, suggesting evolution under strong positive selection. The phylogenies of the viruses and of their tick hosts were not congruent, suggesting recurrent host changes across tick genera during their evolution. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.

Buried Narratives: Exhuming the Mother's Story in Oliver Twist

2018 ◽  
Vol 8 (3) ◽  
pp. 247-266
Author(s):  
Michelle L. Wilson
Keyword(s):  
Social Change ◽  
Maternal Inheritance ◽  
The Novel ◽  
Poor Law ◽  
The Family ◽  
The Law ◽  
First Time ◽  
Critical Consideration

Initially, Oliver Twist (1839) might seem representative of the archetypal male social plot, following an orphan and finding him a place by discovering the father and settling the boy within his inheritance. But Agnes Fleming haunts this narrative, undoing its neat, linear transmission. This reconsideration of maternal inheritance and plot in the novel occurs against the backdrop of legal and social change. I extend the critical consideration of the novel's relationship to the New Poor Law by thinking about its reflection on the bastardy clauses. And here, of course, is where the mother enters. Under the bastardy clauses, the responsibility for economic maintenance of bastard children was, for the first time, legally assigned to the mother, relieving the father of any and all obligation. Oliver Twist manages to critique the bastardy clauses for their release of the father, while simultaneously embracing the placement of the mother at the head of the family line. Both Oliver and the novel thus suggest that it is the mother's story that matters, her name through which we find our own. And by containing both plots – that of the father and the mother – Oliver Twist reveals the violence implicit in traditional modes of inheritance in the novel and under the law.

Faktor-Faktor Determinan yang melatar belakangi Kehamilan Remaja di Desa Pandansari Kecamatan Poncokusumo Kabupaten Malang

2020 ◽  
Vol 7 (2) ◽  
pp. 247-255
Author(s):  
Maria Magdalena Setyaningsih ◽  
Emy Sutiyarsih
Keyword(s):  
Sex Education ◽  
Teen Pregnancy ◽  
Teenage Pregnancy ◽  
Well Being ◽  
Case Control ◽  
Control Group ◽  
Case Group ◽  
The Family ◽  
History Of ◽  
First Time

Kehamilan remaja adalah kehamilan yang terjadi pada remaja berusia kurang dari 20 tahunan. Kehamilan remaja memberikan banyak kerugian bagi kesehatan, mental dan psikologis, kesejahteraan ekonomi dan peluang karier, kemiskinan dan prospek kehidupan masa depan remaja. Tujuan penelitian mengidentifikasi faktor determinan yang melatarbelakangi terjadinya kehamilan remaja. Jenis penelitian adalah penelitian analitik kategorik jenis survei kuantitatif dengan desain case control. Populasi semua perempuan yang bertempat tinggal di wilayah dusun Wonosari, Sukosari, dan Krajan Pandansari dan pernah/sedang hamil pertama kali pada usia kurang dari 20 tahun. Teknik pengambilan sampel cluster random sampling besar sampel 73. Berdasarkan hasil model akhir analisis multivariat, diketahui bahwa variabel pendidikan, riwayat kehamilan remaja pada keluarga dan usia menikah merupakan variabel yang berhubungan dengan kejadian kehamilan remaja setelah dikontrol oleh variabel akses informasi, responden berpendidikan rendah memiliki peluang 20,8 kali lebih tinggi, responden yang memiliki riwayat kehamilan remaja pada keluarga memiliki peluang 14,9 kali lebih tinggi, responden yang menikah pada usia <20 tahun memiliki peluang 12,1 kali lebih tinggi, responden dengan pemahaman yang kurang baik terkait penggunaan kondom memiliki peluang 5,9 kali lebih tinggi untuk terjadi kehamilan remaja. Oleh karena itu perlu dibangun karakter buiding, sosial karakter suport untuk para ibu remaja dan keluarga sehingga terbangun interaksi yang baik dalam keluarga yang dilandasi dengan pendidikan dan pemahaman yang baik tentang Pendidikan seksualitas. Teen pregnancy is a pregnancy that occurs in adolescents aged less than 20 years old. Teen pregnancy provides many disadvantages for health, mental, psychological, economic well-being, career opportunities, poverty, and the future life. The aim of the study was to identify the determinants underlying teen pregnancy incidence. This study was a quantitative study with categorical analytic method. The study design used a case control with two comparison groups. The groups were control group and case group. The population in this study was all women who lived in the Wonosari, Sukosari, and Krajan Pandansari district and had or were pregnant for the first time at the age of less than 20 years old. Seventy three respondents were recruited using cluster sampling technique. The case group consists of women who were or had pregnant for the first time at the age of less than 20 years old and their children are currently aged ≤ 1 years old. The control group consists of women who were pregnant for the first time at the age of > 20 years old. The data was collected using a questionnaire. The findings showed that education, history of teen pregnancy in family and the age of marriage were related to the incidence of teen pregnancy after being controlled by information access. Low-educated respondents had 20.8 times higher chance of experiencing teen pregnancy; respondents with a history of teen pregnancy in the family had 4.9 times higher chance of experiencing teen pregnancy; respondents who were married at the age of < 20 years old had 12.1 times higher chance of experiencing teen pregnancy; respondents with poor understanding of condom use had 5.9 times higher chance of teenage pregnancy. In conclusion, the findings suggest to build good interactions in the family based on education and a good understanding of sex education.

New records of some rare species in the family Hyaloscyphaceae (Ascomycota, Helotiales) from Central Russia

2013 ◽  
Vol 47 ◽  
pp. 135-142
Author(s):  
E. S. Popov
Keyword(s):  
Rare Species ◽  
New Records ◽  
Moscow Region ◽  
North Caucasus ◽  
Central Russia ◽  
The Family ◽  
First Time

Three rare species of discomycetes in the family Hyaloscyphaceae are reported from Central Russia (Oryol and Bryansk Regions). Proliferodiscus tricolor is recorded for the first time in Russia. Comments are made on Aeruginoscyphus sericeus and Eriopezia caesia previously reported only from Moscow Region and North Caucasus respectively.

Contribution to the flora of marine algae of the coastal zone of the northeastern part of the Sea of Okhotsk

2018 ◽  
Vol 52 (1) ◽  
pp. 63-73
Author(s):  
N. V. Evseeva
Keyword(s):  
Coastal Zone ◽  
Sea Of Okhotsk ◽  
Marine Algae ◽  
Herbarium Material ◽  
Northeastern Part ◽  
The Sea Of Okhotsk ◽  
The Family ◽  
First Time

The revision of the herbarium material, collected in the northern part of the Sea of Okhotsk in 1965–1966 and stored in VNIRO, allowed to expand the taxonomic list of macrophyte algae of the coastal zone of this area. The locations of discovery of 24 previously unmentioned species are described. Myrionema balticum, Ulvella repens, Syncoryne reinkei, Acrochaetium arcuatum were found in the Sea of Okhotsk for the first time. Most species new for the Sea of Okhotsk is represented by epiphytes of the family Ulvellaceae (Chlorophyta). The final taxonomic list of this region, including literature data, consists of 169 species.

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