scholarly journals Hybridization in Selected Species and Genera of Diaptomid Copepods in China

Water ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1181
Author(s):  
Hui-Ming Li ◽  
Ping Liu ◽  
Xiao-Li Zhang ◽  
Henri J. Dumont ◽  
Bo-Ping Han
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Genetic Distances ◽  
Intergeneric Hybridization ◽  
Cryptic Speciation ◽  
Calanoid Copepods ◽  
Mitochondrial Coi ◽  
Different Populations ◽  
First Time ◽  
Hybridization And Introgression

To better understand the fauna of freshwater calanoid copepods of China, including the occurrence of intra- and intergeneric hybridization, we studied five species, distributed across the whole of China or in South China. We sequenced a mitochondrial (COI) and the nuclear ribosome 18S operon (ITS) to reconstruct the phylogenetic trees by using a Bayesian and maximum likelihood (ML) approach with 161 individuals. The phylogeny tree revealed five clades and two geographically separated subclades in both S. ferus and P. tunguidus. We found, for the first time, that the hybrid specimens occurred in Diaptomidae, but low hybridization suggested effective barriers to hybridization and introgression. One hypothesis, that hybridization is recent and was initiated by invasions via canals built between the Yangtze and Pearl rivers c. 2000 years ago, is not supported by K2P genetic distances of the order of 20%. Furthermore, COI analysis of different populations of S. ferus and P. tunguidus revealed two geographical clades in each species, with genetic distances commensurate with cryptic speciation. Both clades occupy subranges maintained without visible barriers to mixis.

Diaphanocephalus galeatus (Nematoda: Diaphanocephalidae), a poorly known parasite of lizards: redescription, first genetic characterization and a revision of its congeners from Brazil

2018 ◽  
Vol 93 (05) ◽  
pp. 629-635
Author(s):  
F.B. Pereira ◽  
V.L. Ferreira ◽  
W.M. Tomas ◽  
C. Elisei ◽  
F. Paiva ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Genetic Characterization ◽  
Nuclear Gene ◽  
Buccal Capsule ◽  
Morphological Characterization ◽  
28S Rrna ◽  
Type Specimens ◽  
Mato Grosso ◽  
Different Populations ◽  
First Time

AbstractDiaphanocephalus galeatus collected from the small intestine of the lizard Dracaena paraguayensis in the Pantanal wetlands, State of Mato Grosso do Sul, Brazil, is redescribed. Genetic characterization and observations using scanning electron microscopy (SEM) were performed for the first time. The vouchers of D. galeatus and the type specimens of its congeners, deposited in the Coleção Helmintológica do Instituto Oswaldo Cruz (CHIOC), were consulted. Light and SEM observations revealed several undescribed features of D. galeatus, i.e. structure of the cephalic end and of the buccal capsule, position and morphology of deirids, presence of phasmids in females and presence of unpaired papilla on the membranous projection that covers the genital cone in males. After observation of the specimens deposited in the helminthological collection, D. jacuruxi is considered a synonym of D. galeatus, and D. diesingi, despite its incomplete description, is tentatively retained as valid due to the poor condition of the type material. The results also indicated low host specificity of D. galeatus, contradicting previous assertions. Genetic comparisons using patristic distances and phylogenetic trees generated from sequences of the 28S rRNA nuclear gene indicated that D. galeatus is closer to the taxa within Ancylostomatoidea and Strongyloidea than any lineage of Metastrongyloidea or Trichostrongyloidea. However, most of the nodal supports were low. Based on the genetic and morphological characterization, the validity of D. galeatus was confirmed. These data may serve for further comparative approaches for different populations of the parasite, from different hosts in different geographical areas, mitigating taxonomic confusions.

scholarly journals DNA Barcoding of Fish in Mischief Reef—Fish Diversity of a Reef Fish Community From Nansha Islands

2021 ◽  
Vol 7 ◽  
Author(s):  
Binbin Shan ◽  
Yan Liu ◽  
Changping Yang ◽  
Yu Zhao ◽  
Gongjun Zhang ◽  
...  
Keyword(s):  
Reef Fish ◽  
Management Strategies ◽  
Genetic Distances ◽  
Coi Gene ◽  
Fish Diversity ◽  
Nansha Islands ◽  
Mitochondrial Coi ◽  
Mitochondrial Coi Gene ◽  
First Time ◽  
Effective Conservation

Development of effective conservation and management strategies requires assessments of ecosystem biodiversity status, especially in understudied hotspots of global fish diversity. Coral reefs are important habitats for fishes, with biodiversity hotspots known globally. We present the first data on molecular diversity of fishes of Mischief Reef, the largest atoll in the Nansha Islands. Partial sequences (650 bp) of mitochondrial COI gene (Cytochrome c oxidase subunit I) are used to identify 209 individuals, representing 101 species, referable to 62 genera, 27 families, 8 orders, and 1 class. The most abundant orders are the Perciformes (176 specimens, 84.21%), Tetraodontiformes (13 specimens, 6.22%), and Beryciformes (13 specimens, 6.22%). Mean Kimura 2-Parameter genetic distances within genera, families, and orders are 4.51, 13.90, and 17.63%, respectively. We record Monotaxis heterodon from this region for the first time—a species that may previously have been misidentified as M. grandoculis. In addition, we recognized possible cryptic species of Lethrinus olivaceus based on significantly diverging barcode sequences. Barcode data provide new insights into fish diversity of Mischief Reef, important for developing further researches on this fauna, and for its conservation.

scholarly journals Genomic Epidemiology of SARS-CoV-2 Divulge B.1, B.1.36, and B.1.1.7 as the Most Dominant Lineages in First, Second, and Third Wave of SARS-CoV-2 Infections in Pakistan

2021 ◽  
Vol 9 (12) ◽  
pp. 2609
Author(s):  
Atia Basheer ◽  
Imran Zahoor
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Reference Genome ◽  
Third Wave ◽  
Genomic Epidemiology ◽  
Wave Data ◽  
The World ◽  
Reference Sequences ◽  
First Time ◽  
Second Wave

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with its role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain and coverage map was created by employing Nextclade. By using the amino acid substitutions, the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following seven clades G, GH, GR, GRY, L, O, and S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), and B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%), and B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of nine lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), and Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.

scholarly journals Genomic epidemiology of SARS-CoV-2 divulge B.1, B.1.36, and B.1.1.7 as the most dominant lineages in first, second, and third wave of SARS-CoV-2 infections in Pakistan

2021 ◽  
Author(s):  
Atia Basheer ◽  
Imran Zahoor
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Reference Genome ◽  
Third Wave ◽  
Genomic Epidemiology ◽  
Wave Data ◽  
The World ◽  
Reference Sequences ◽  
First Time ◽  
Second Wave

The present study aims to investigate the genomic variability and epidemiology of SARS-CoV-2 in Pakistan along with their role in the spread and severity of infection during the three waves of COVID-19. A total of 453 genomic sequences of Pakistani SARS-CoV-2 were retrieved from GISAID and subjected to MAFFT-based alignment and QC check which resulted in removal of 53 samples. The remaining 400 samples were subjected to Pangolin-based genomic lineage identification. And to infer our SARS-CoV-2 time-scaled and divergence phylogenetic trees, 3,804 selected global reference sequences plus 400 Pakistani samples were used for the Nextstrain analysis with Wuhan/Hu-1/2019, as reference genome. Finally, maximum likelihood based phylogenetic tree was built by using the Nextstrain & coverage map was created by employing Nextclade. And by using the amino acid subsitutions the maximum likelihood phylogenetic trees were developed for each wave, separately. Our results reveal the circulation of 29 lineages, belonging to following 7 clades G, GH, GR, GRY, L, O, & S in the three waves. From first wave, 16 genomic lineages of SARS-CoV-2 were identified with B.1(24.7%), B.1.36(18.8%), & B.1.471(18.8%) as the most prevalent lineages respectively. The second wave data showed 18 lineages, 10 of which were overlapping with the first wave suggesting that those variants could not be contained during the first wave. In this wave, a new lineage, AE.4, was reported from Pakistan for the very first time in the world. However, B.1.36 (17.8%), B.1.36.31 (11.9%), B.1.1.7 (8.5%) & B.1.1.1 (5.9%) were the major lineages in second wave. Third wave data showed the presence of 9 lineages with Alpha/B.1.1.7 (72.7%), Beta/B.1.351 (12.99%), & Delta/B.1.617.2 (10.39%) as the most predominant variants. It is suggested that these VOCs should be contained at the earliest in order to prevent any devastating outbreak of SARS-CoV-2 in the country.

scholarly journals DNA barcoding of aphid-associated ants (Hymenoptera, Formicidae) in a subtropical area of southern China

ZooKeys ◽  
2019 ◽  
Vol 879 ◽  
pp. 117-136
Author(s):  
Junaid Ali Siddiqui ◽  
Zhilin Chen ◽  
Qiang Li ◽  
Jun Deng ◽  
Xiaolan Lin ◽  
...  
Keyword(s):  
Southern China ◽  
Dna Barcode ◽  
Genetic Distances ◽  
Reference Library ◽  
Mitochondrial Coi ◽  
Subtropical Area ◽  
Tetramorium Bicarinatum ◽  
Coi Sequences ◽  
Terrestrial Insects ◽  
First Time

As one of the most abundant and complex groups of terrestrial insects, ants have associations with many other organismal groups, such as hemipteran insects producing honeydew. With the aim of expanding the knowledge base of ant species associated with aphids, this study analyzed mitochondrial COI barcodes of 301 ant samples for 37 aphid-associated ant species in a subtropical area of southern China. Sequence analyses revealed that the intraspecific and interspecific distances ranged from zero to 7.7%% and 0.2 to 31.7%, respectively. Three barcoding approaches – Automatic Barcode Gap Discovery, Bayesian Poisson Tree Processes and Generalized Mixed Yule-coalescent – were used to help delimit ant species based on COI sequences, and their results corresponded well with most of the morphospecies. All three approaches indicate cryptic diversity may exist within Tetramorium bicarinatum and Technomyrmex albipes, with intraspecific genetic distances of 7.7% and 6.24%, respectively. Our analyses also reported five species for the first time from Fujian Province of China, and the COI sequences of nine species are newly added into the GenBank. This study provides information about species diversity of aphid-associated ants in subtropical China and compiles a DNA barcode reference library for future ant barcoding work.

Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?

2012 ◽  
Vol 39 (2) ◽  
pp. 217-233 ◽  
Author(s):  
J. David Archibald
Keyword(s):  
Fossil Record ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Charles Darwin ◽  
The Other ◽  
Charles Lyell ◽  
Single Origin ◽  
Molecular Studies ◽  
Richard Owen ◽  
First Time

Studies of the origin and diversification of major groups of plants and animals are contentious topics in current evolutionary biology. This includes the study of the timing and relationships of the two major clades of extant mammals – marsupials and placentals. Molecular studies concerned with marsupial and placental origin and diversification can be at odds with the fossil record. Such studies are, however, not a recent phenomenon. Over 150 years ago Charles Darwin weighed two alternative views on the origin of marsupials and placentals. Less than a year after the publication of On the origin of species, Darwin outlined these in a letter to Charles Lyell dated 23 September 1860. The letter concluded with two competing phylogenetic diagrams. One showed marsupials as ancestral to both living marsupials and placentals, whereas the other showed a non-marsupial, non-placental as being ancestral to both living marsupials and placentals. These two diagrams are published here for the first time. These are the only such competing phylogenetic diagrams that Darwin is known to have produced. In addition to examining the question of mammalian origins in this letter and in other manuscript notes discussed here, Darwin confronted the broader issue as to whether major groups of animals had a single origin (monophyly) or were the result of “continuous creation” as advocated for some groups by Richard Owen. Charles Lyell had held similar views to those of Owen, but it is clear from correspondence with Darwin that he was beginning to accept the idea of monophyly of major groups.

The identification of a novel HIV-1 second-generation recombinant form (CRF01_AE/CRF07_BC) among men who have sex with men in Jiangsu, China

2020 ◽  
Vol 18 ◽  
Author(s):  
Yin Yueqi ◽  
Zhou Ying ◽  
Lu Jing ◽  
Guo Hongxiong ◽  
Chen Jianshuang ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Second Generation ◽  
Emergency Situation ◽  
The World ◽  
Break Points ◽  
Sex With Men ◽  
Full Length Genome ◽  
Virus Strains ◽  
Hiv 1

Background: CRF01_AE and CRF07_BC are the two major HIV-1 virus strains circulating in China. The proportion of dominant subtypes (CRF01_AE and CRF07_BC) among MSM in Jiangsu province was over 80%. A large number of URFs have been found in China in recently years. Objective: This study aimed to report on novel HIV-1 recombinants. Method: We constructed Phylogenetic trees using the maximum likelihood (ML) method with 1000 bootstrap replicates in IQ-TREE 1.6.8 software and determined recombination break points using SimPlot 3.5.1. Results: We identified a novel, second-generation HIV-1 recombinant (JS020202) between CRF01_AE and CRF07_BC. The analysis of near full-length genome (NFLG) showed there were at least 8 breakpoints inner virus, which differed from any previously identified CRF and URF around the world. Conclusion: Novel diverse CRF01_AE/07_BC suggested the complexity trends of HIV-1 genetics. The emergency situation of diverse recombinant strains should be monitored continuously.

scholarly journals 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 ◽  
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.

scholarly journals Four new Micarea species from the montane cloud forests of Taita Hills, Kenya

2021 ◽  
Vol 53 (1) ◽  
pp. 81-94
Author(s):  
Annina Kantelinen ◽  
Marko-Tapio Hyvärinen ◽  
Paul M. Kirika ◽  
Leena Myllys
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
Maximum Parsimony ◽  
Polarized Light ◽  
Eastern Arc Mountains ◽  
Brown Pigment ◽  
Cloud Forests ◽  
Taita Hills ◽  
First Time ◽  
Existing Data

AbstractThe genus Micarea was studied for the first time in the Taita Hills, Kenya. Based on new collections and existing data, we reconstructed a phylogeny using ITS, mtSSU and Mcm7 regions, and generated a total of 27 new sequences. Data were analyzed using maximum likelihood and maximum parsimony methods. Based mainly on new collections, we discovered four undescribed well-supported lineages, characterized by molecular and phenotypic features. These lineages are described here as Micarea pumila, M. stellaris, M. taitensis and M. versicolor. Micarea pumila is characterized by a minutely granular thallus, small cream-white or pale brownish apothecia, small ascospores and the production of prasinic acid. Micarea stellaris has a warted-areolate thallus, cream-white apothecia usually darker at the centre, a hymenium of light grey or brownish pigment that dissolves in K, and intense crystalline granules that appear as a belt-like continuum across the lower hymenium when studied in polarized light. Micarea taitensis is characterized by a warted-areolate thallus and cream-white or yellowish apothecia that sometimes produce the Sedifolia-grey pigment. Micarea versicolor is characterized by a warted-areolate, sometimes partly granular thallus and apothecia varying from cream-white to light grey to blackish in colour. This considerable variation in the coloration of its apothecia is caused by an occasional mixture of the Sedifolia-grey pigment in the epihymenium and another purplish brown pigment in the hymenium. Micarea stellaris, M. taitensis and M. versicolor produce methoxymicareic acid. The main distinguishing characters are presented in a species synopsis. Three of the new species are nested in the M. prasina group, and the fourth one (M. taitensis) resolves as a basal taxon to the M. prasina group. The new species inhabit montane cloud forests, which have fragmented dramatically throughout the Eastern Arc Mountains in recent decades.

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