A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): Evolutionary and taxonomic implications

Arvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.

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A mitochondrial genome phylogeny of voles and lemmings (Rodentia: Arvicolinae): evolutionary and taxonomic implications

10.1101/2021.02.23.432437 ◽

2021 ◽

Author(s):

Natalia I. Abramson ◽

Semyon Yu. Bodrov ◽

Olga V. Bondareva ◽

Evgeny A. Genelt-Yanovskiy ◽

Tatyana V. Petrova

Keyword(s):

Molecular Dating ◽

Tree Reconstruction ◽

Protein Coding ◽

Weak Support ◽

Full Resolution ◽

Genome Phylogeny ◽

Taxonomic Implications ◽

Complex Relationships ◽

Fossil Records ◽

First Time

AbstractArvicolinae is one of the most impressive placental radiations with over 150 extant and numerous extinct species that emerged since the Miocene in the Northern Hemisphere. The phylogeny of Arvicolinae has been studied intensively for several decades using morphological and genetic methods. Here, we sequenced 30 new mitochondrial genomes to better understand the evolutionary relationships among the major tribes and genera within the subfamily. The phylogenetic and molecular dating analyses based on 11,391 bp concatenated alignment of protein-coding mitochondrial genes confirmed the monophyly of the subfamily. While Bayesian analysis provided a high resolution across the entire tree, Maximum Likelihood tree reconstruction showed weak support for the ordering of divergence and interrelationships of tribal level taxa within the most ancient radiation. Both the interrelationships among tribes Lagurini, Ellobiusini and Arvicolini, comprising the largest radiation and the position of the genus Dinaromys within it also remained unresolved. For the first time complex relationships between genus level taxa within the species-rich tribe Arvicolini received full resolution. Particularly Lemmiscus was robustly placed as sister to the snow voles Chionomys in the tribe Arvicolini in contrast with a long-held belief of its affinity with Lagurini. Molecular dating of the origin of Arvicolinae and early divergences obtained from the mitogenome data were consistent with fossil records. The mtDNA estimates for putative ancestors of the most genera within Arvicolini appeared to be much older than it was previously proposed in paleontological studies.

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Sequencing of Organellar Genomes of Nowellia curvifolia (Cephaloziaceae Jungermanniales) Revealed the Smallest Plastome with Complete Gene Set and High Intraspecific Variation Suggesting Cryptic Speciation

Diversity ◽

10.3390/d13020081 ◽

2021 ◽

Vol 13 (2) ◽

pp. 81

Author(s):

Jakub Sawicki ◽

Katarzyna Krawczyk ◽

Monika Ślipiko ◽

Monika Szczecińska

Keyword(s):

Cryptic Speciation ◽

Editing Event ◽

Protein Coding ◽

Gene Set ◽

Protein Coding Genes ◽

Organellar Genomes ◽

The Family ◽

Leafy Liverwort ◽

Aneura Mirabilis ◽

First Time

The leafy liverwort Nowellia curvifolia is a widespread Holarctic species belonging to the family Cephaloziaceae. It is made up of a newly sequenced, assembled and annotated organellar genomes of two European specimens, which revealed the structure typical for liverworts, but also provided new insights into its microevolution. The plastome of N. curvifolia is the second smallest among photosynthetic liverworts, with the shortest known inverted repeats. Moreover, it is the smallest liverwort genome with a complete gene set, since two smaller genomes of Aneura mirabilis and Cololejeunea lanciloba are missing six and four protein-coding genes respectively. The reduction of plastome size in leafy liverworts seems to be mainly impacted by deletion within specific region between psbA and psbD genes. The comparative intraspecific analysis revealed single SNPs difference among European individuals and a low number of 35 mutations differentiating European and North American specimens. However, the genetic resources of Asian specimen enabled to identify 1335 SNPs in plastic protein-coding genes suggesting an advanced cryptic speciation within N. curvifolia or the presence of undescribed morphospecies in Asia. Newly sequenced mitogenomes from European specimens revealed identical gene content and structure to previously published and low intercontinental differentiation limited to one substitution and three indels. The RNA-seq based RNA editing analysis revealed 17 and 127 edited sites in plastome and mitogenome respectively including one non-canonical editing event in plastid chiL gene. The U to C editing is common in non-seed plants, but in liverwort plastome is reported for the first time.

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Potential for transmission of Elizabethkingia anophelis by Aedes albopictus and the role of microbial interactions in Zika virus competence

10.1101/702464 ◽

2019 ◽

Author(s):

MG Onyango ◽

AF Payne ◽

J Stout ◽

C Dieme ◽

L Kuo ◽

...

Keyword(s):

Zika Virus ◽

Inhibitory Effect ◽

Microbial Interactions ◽

Morbidity And Mortality ◽

Source Of Infection ◽

Vector Borne ◽

Complex Relationships ◽

The Impact ◽

First Time ◽

Transmission Barrier

AbstractElizabethkingia anophelis has been the cause of four outbreaks with significant morbidity and mortality. Its transmission routes remain unknown and no point source of infection has been identified. Here we show that E. anophelis can be found in the saliva of Aedes mosquitoes, suggesting the novel possibility of vector-borne transmission of this bacterium. We additionally characterized diverse microbial communities in Aedes midguts, salivary glands and saliva. To the best of our knowledge, this represents the first description of the microbiome of Aedes saliva. Further, we demonstrate that increased abundance of E. anophelis is associated with decreased susceptibility and replication of Zika virus (ZIKV) in the midgut of Aedes mosquitoes, suggesting a novel transmission barrier for arboviruses transmitted by Aedes mosquitoes. Together, these results demonstrate the complex relationships between the mosquito, the midgut microbial community and arboviruses and offer insights into the epidemiology and control of emerging bacterial and viral pathogens.Author SummaryElizabethkingia anophelis has in the recent past caused outbreaks different parts of the world resulting both in morbidity and mortality. Until now, to the best of our knowledge, no study has been able to demonstrate that this bacterium can be transmitted by mosquitoes. We have demonstrated for the first time that Elizabethkingia anophelis is present in the saliva of both infected and non-infected Aedes mosquitoes. Further, we have shown that it confers an inhibitory effect on Zika virus establishment in the midguts of Aedes mosquitoes. Together, these results potentially display the potential for vector borne transmission of E. anophelis as well as a novel transmission barrier of ZIKV. Lastly, we have for the first time characterized salivary microbes of Aedes mosquitoes necessitating the investigation of the impact of salivary microbes in severity of disease in vertebrate hosts.

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Comparative cytogenetics of two species of Dermanura (Chiroptera, Phyllostomidae) in Midwestern Brazil

Comparative Cytogenetics ◽

10.3897/compcytogen.v15i2.60577 ◽

2021 ◽

Vol 15 (2) ◽

pp. 89-99

Author(s):

Ricardo Firmino de Sousa ◽

Paulo Cesar Venere ◽

Karina de Cassia Faria

Keyword(s):

Diploid Number ◽

Constitutive Heterochromatin ◽

Sex Chromosome ◽

Type System ◽

Pericentromeric Region ◽

Morphological Characters ◽

Comparative Cytogenetics ◽

Taxonomic Implications ◽

Sex Chromosome System ◽

First Time

Dermanura Gervais, 1856 is represented by small frugivorous bats of the Stenodermatinae subfamily. The taxonomy of this group presents controversies and has been subject to changes, especially since the morphological characters evaluated have left gaps that are difficult to fill regarding good species characterization. Previous studies performed in Dermanura cinerea Gervais, 1856 found that the karyotype of this species has a diploid number of chromosomes equal to 30 and 56 autosomal arms. The objective of the present study was to describe, for the first time, the karyotypes of the species Dermanura anderseni (Osgood, 1916) and Dermanura gnoma (Handley, 1987) based on classical cytogenetic markers. For both species, the diploid number found was 2n = 30 and NFa = 56. Two pairs of chromosomes showed markings of the nucleolus organizing regions (AgNORs) in the species D. anderseni and only one pair in D. gnoma, differing from what has already been described for D. cinerea. The two species analyzed here also showed differences in the sex chromosome system, with D. gnoma showing a neo-XY type system while in D. anderseni the classic XY sexual system was observed. In both species, visualization of the constitutive heterochromatin occurred in the pericentromeric region of all chromosomes, as well as in the short arms of the subtelocentric chromosomes. The present work represents an important expansion of karyotypic information for the subfamily Stenodermatinae, bringing chromosomal features that are possible to use in the taxonomic implications of the group.

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Relationship between Religious Orientation and Love Styles, Sexual Attitudes, and Sexual Behaviors

Journal of Psychology and Theology ◽

10.1177/009164719302100405 ◽

1993 ◽

Vol 21 (4) ◽

pp. 315-318 ◽

Cited By ~ 8

Author(s):

Gary K. Leak

Keyword(s):

Sexual Behavior ◽

Sexual Behaviors ◽

Religious Orientation ◽

Sexual Attitudes ◽

Conservative Approach ◽

Love Styles ◽

Complex Relationships ◽

First Time

This research had two objectives: (a) to extend our understanding of the sexual behavior, attitudes, and love styles of religiously mature and immature individuals using recent measures of love styles and sexual attitudes and (b) to investigate, for the first time, the sexual and love correlates of the quest religious orientation. The results are consistent with prior research using other measures, and they suggest that intrinsically religious individuals are highly discriminating in their conservative approach to sexuality, while extrinsics are somewhat self-serving. While only exploratory, these results should encourage scholars and practitioners to appreciate the highly complex relationships between religiosity and sexuality, and that global statements (e.g., religious individuals are sexually conservative) need to take into account a particular individual's religious orientation as well as the nature of the sexual dimension being considered.

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Mitochondrial DNA dataset suggest that the genus Sphaerirostris Golvan, 1956 is a synonym of the genus Centrorhynchus Lühe, 1911

Parasitology ◽

10.1017/s0031182020000906 ◽

2020 ◽

Vol 147 (10) ◽

pp. 1149-1157 ◽

Cited By ~ 1

Author(s):

Nehaz Muhammad ◽

Suleman ◽

Munawar Saleem Ahmad ◽

Liang Li ◽

Qing Zhao ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Systematic Position ◽

Likelihood Methods ◽

Sister Relationship ◽

Protein Coding ◽

Maximum Likelihood Methods ◽

Relationship Of ◽

First Time ◽

Mt Genome ◽

Rna Genes

AbstractOur present genetic data of Acanthocephala, especially the mitochondrial (mt) genomes, remains very limited. In the present study, the nearly complete mt genome sequences of Sphaerirostris lanceoides (Petrochenko, 1949) was sequenced and determined for the first time based on specimens collected from the Indian pond heron Ardeola grayii (Sykes) (Ciconiiformes: Ardeidae) in Pakistan. The mt genome of S. lanceoides is 13 478 bp in size and contains 36 genes, including 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Moreover, in order to clarify the phylogenetic relationship of the genera Centrorhynchus and Sphaerirostris, and to test the systematic position of S. lanceoides in the Centrorhynchidae, the phylogenetic analyses were performed using Bayesian inference and maximum likelihood methods, based on concatenated nucleotide sequences of 12 PCGs, rRNAs and tRNAs. The phylogenetic results further confirmed the monophyly of the order Polymorphida and the paraphyly of the order Echinorhynchida in the class Palaeacanthocephala. Our results also challenged the validity of the genus Sphaerirostris (Polymorphida: Centrorhynchidae) and showed a sister relationship between S. lanceoides and S. picae (Rudolphi, 1819).

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Seed testa sculpture of species of Allium L. (Amaryllidaceae) and its taxonomic implications

Turczaninowia ◽

10.14258/turczaninowia.24.1.17 ◽

2021 ◽

Vol 24 (1) ◽

pp. 154-161

Author(s):

Shukherdorj Baasanmunkh ◽

Hyeok Jae Choi ◽

Batlai Oyuntsetseg ◽

Nilolay V. Friesen

Keyword(s):

Anticlinal Wall ◽

Periclinal Wall ◽

Dense Granules ◽

Taxonomic Implications ◽

First Time ◽

Important Character ◽

Seed Testa

We investigated the seed testa sculpture of twenty-four species belonging to thirteen sections and five subgenera of Allium from the herbarium materials or collected from plants in living collections. Seed testa sculpture of 21 species were described for the first time in this study. According to our results, the straight anticlinal wall and one large verruca or dense granules periclinal wall were found among the species in subgenus Amerallium, Cepa, Polyprason and Reticulatobulbosa. Only A. ochroleucum (sect. Daghestanica, subg. Polyprason) has U-type undulation anticlinal wall, which is similar to species of subg. Allium. The U- to Omega-type undulation anticlinal walls and several big verrucae with marginal verrucae periclinal wall were found in subg. Allium. Our results suggest that seed testa sculpture is important character of species and sections level of the genus Allium.

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Structure and Phylogeny of the Curly Birch Chloroplast Genome

Frontiers in Genetics ◽

10.3389/fgene.2021.625764 ◽

2021 ◽

Vol 12 ◽

Author(s):

Konstantin A. Shestibratov ◽

Oleg Yu. Baranov ◽

Eugenia N. Mescherova ◽

Pavel S. Kiryanov ◽

Stanislav V. Panteleev ◽

...

Keyword(s):

Chloroplast Genome ◽

Genetic Markers ◽

De Novo ◽

Functional Organization ◽

Protein Coding ◽

Organelle Genomes ◽

Genes Encoding ◽

Cpdna Sequence ◽

Ssr Loci ◽

First Time

Curly birch [Betula pendula var. carelica (Merckl.) Hämet-Ahti] is a relatively rare variety of silver birch (B. pendula Roth) that occurs mainly in Northern Europe and northwest part of Russia (Karelia). It is famous for the beautiful decorative texture of wood. Abnormal xylogenesis underlying this trait is heritable, but its genetic mechanism has not yet been fully understood. The high number of potentially informative genetic markers can be identified through sequencing nuclear and organelle genomes. Here, the de novo assembly, complete nucleotide sequence, and annotation of the chloroplast genome (plastome) of curly birch are presented for the first time. The complete plastome length is 160,523 bp. It contains 82 genes encoding structural and enzymatic proteins, 37 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The chloroplast DNA (cpDNA) is AT-rich containing 31.5% of A and 32.5% of T nucleotides. The GC-rich regions represent inverted repeats IR1 and IR2 containing genes of rRNAs (5S, 4.5S, 23S, and 16S) and tRNAs (trnV, trnI, and trnA). A high content of GC was found in rRNA (55.2%) and tRNA (53.2%) genes, but only 37.0% in protein-coding genes. In total, 384 microsatellite or simple sequence repeat (SSR) loci were found, mostly with mononucleotide motifs (92% of all loci) and predominantly A or T motifs (94% of all mononucleotide motifs). Comparative analysis of cpDNA in different plant species revealed high structural and functional conservatism in organization of the angiosperm plastomes, while the level of differences depends on the phylogenetic relationship. The structural and functional organization of plastome in curly birch was similar to cpDNA in other species of woody plants. Finally, the identified cpDNA sequence variation will allow to develop useful genetic markers.

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Revised phylogenetic analysis of the Aetosauria (Archosauria: Pseudosuchia); assessing the effects of incongruent morphological character sets

PeerJ ◽

10.7717/peerj.1583 ◽

2016 ◽

Vol 4 ◽

pp. e1583 ◽

Cited By ~ 24

Author(s):

William G. Parker

Keyword(s):

Phylogenetic Analysis ◽

Convergent Evolution ◽

Morphological Character ◽

Late Triassic ◽

Parsimony Analysis ◽

Weak Support ◽

Selective Pressures ◽

Body Regions ◽

High Species Diversity ◽

First Time

Aetosauria is an early-diverging clade of pseudosuchians (crocodile-line archosaurs) that had a global distribution and high species diversity as a key component of various Late Triassic terrestrial faunas. It is one of only two Late Triassic clades of large herbivorous archosaurs, and thus served a critical ecological role. Nonetheless, aetosaur phylogenetic relationships are still poorly understood, owing to an overreliance on osteoderm characters, which are often poorly constructed and suspected to be highly homoplastic. A new phylogenetic analysis of the Aetosauria, comprising 27 taxa and 83 characters, includes more than 40 new characters that focus on better sampling the cranial and endoskeletal regions, and represents the most comprenhensive phylogeny of the clade to date. Parsimony analysis recovered three most parsimonious trees; the strict consensus of these trees finds an Aetosauria that is divided into two main clades: Desmatosuchia, which includes the Desmatosuchinae and the Stagonolepidinae, and Aetosaurinae, which includes the Typothoracinae. As defined Desmatosuchinae now containsNeoaetosauroides engaeusand several taxa that were previously referred to the genusStagonolepis, and a new clade, Desmatosuchini, is erected for taxa more closely related toDesmatosuchus. Overall support for some clades is still weak, and Partitioned Bremer Support (PBS) is applied for the first time to a strictly morphological dataset demonstrating that this weak support is in part because of conflict in the phylogenetic signals of cranial versus postcranial characters. PBS helps identify homoplasy among characters from various body regions, presumably the result of convergent evolution within discrete anatomical modules. It is likely that at least some of this character conflict results from different body regions evolving at different rates, which may have been under different selective pressures.

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Genome Sequencing of a Novel Coronavirus SARS-CoV-2 Isolate from Iraq

Microbiology Resource Announcements ◽

10.1128/mra.01316-20 ◽

2021 ◽

Vol 10 (4) ◽

Author(s):

Nihad A. M. Al-Rashedi ◽

Danilo Licastro ◽

Sreejith Rajasekharan ◽

Simeone Dal Monego ◽

Alessandro Marcello ◽

...

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Genome Sequencing ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Illumina Miseq ◽

Spike Protein ◽

Protein Coding ◽

Novel Coronavirus ◽

First Time

ABSTRACT The coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain isolated from an Iraqi patient was sequenced for the first-time using Illumina MiSeq technology. There was a D614G mutation in the spike protein-coding sequence. This report is valuable for better understanding the spread of the virus in Iraq.

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