Near-complete phylogeny of extant Crocodylia (Reptilia) using mitogenome-based data

2020 ◽  
Author(s):  
Tao Pan ◽  
Jia-Shun Miao ◽  
Hua-Bin Zhang ◽  
Peng Yan ◽  
Ping-Shin Lee ◽  
...  
Keyword(s):  
Upper Cretaceous ◽  
Phylogenetic Analyses ◽  
Decisive Role ◽  
Late Eocene ◽  
Molecular Dating ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
Late Cretaceous Period ◽  
Climate Fluctuation ◽  
Cretaceous Period

Abstract Species of the order Crocodylia are mostly large, predatory and semi-aquatic reptiles. Crocodylia, the closest living relatives of birds, first appeared in the Late Cretaceous period. In the present study, the complete mitochondrial (mt) genomes of 19 Crocodylia species, including two species (Melanosuchus niger and Caiman yacare) that have not been previously sequenced for mitogenomes, were processed through Illumina sequencing to offer genetic resources and compare with the mitogenomes of Crocodylia species reported previously. In addition, a high-resolution phylogenetic tree of nearly all current recognized species of Crocodylia is constructed based on mitogenomic data. Phylogenetic analyses support monophyly of three families: Alligatoridae (four genera: Alligator, Caiman, Melanosuchus and Paleosuchus), Crocodylidae (three genera: Crocodylus, Mecistops and Osteolaemus) and Gavialidae (two genera: Gavialis and Tomistoma). The tree topology is generally similar to previous studies. Molecular dating suggests that the first split within Crocodylia date back to the Upper Cretaceous (approx. 86.75 Mya). The estimated time to the most recent common ancestor (TMRCA) of Alligatoridae is 53.33 Mya and that of Crocodylidae and Gavialidae is 50.13 Mya, which might be closely linked to climate changes during the Late Palaeocene and Early Eocene. Additionally, this study proves that the diversification rate within Crocodylia began to increase from the Late Eocene (about 36 Mya) and two diversification peak periods of Crocodylia (0–10 Mya and 10–20 Mya) are disclosed, which is roughly consistent with the estimated crocodylian species richness through time. Combining all these clues, we can suggest that climate fluctuation may have played a decisive role in the speciation of Crocodylia.

scholarly journals Phylogenetic and genetic characterization of Treponema pallidum strains from syphilis patients in Japan by whole-genome sequence analysis from global perspectives

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shingo Nishiki ◽  
Kenichi Lee ◽  
Mizue Kanai ◽  
Shu-ichi Nakayama ◽  
Makoto Ohnishi
Keyword(s):  
Genetic Difference ◽  
Phylogenetic Analyses ◽  
Treponema Pallidum ◽  
Whole Genome Sequence ◽  
Epidemiological Surveillance ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Global Perspectives ◽  
Most Recent Common Ancestor ◽  
Sex With Men

AbstractJapan has had a substantial increase in syphilis cases since 2013. However, research on the genomic features of the Treponema pallidum subspecies pallidum (TPA) strains from these cases has been limited. Here, we elucidated the genetic variations and relationships between TPA strains in Japan (detected between 2014 and 2018) and other countries by whole-genome sequencing and phylogenetic analyses, including syphilis epidemiological surveillance data and information on patient sexual orientation. Seventeen of the 20 strains in Japan were SS14- and the remaining 3 were Nichols-lineage. Sixteen of the 17 SS14-lineage strains were classified into previously reported Sub-lineage 1B. Sub-lineage 1B strains in Japan have formed distinct sub-clusters of strains from heterosexuals and strains from men who have sex with men. These strains were closely related to reported TPA strains in China, forming an East-Asian cluster. However, those strains in these countries evolved independently after diverging from their most recent common ancestor and expanded their genetic diversity during the time of syphilis outbreak in each country. The genetic difference between the TPA strains in these countries was characterized by single-nucleotide-polymorphism analyses of their penicillin binding protein genes. Taken together, our results elucidated the detailed phylogenetic features and transmission networks of syphilis.

scholarly journals A FOUNDER EFFECT LED EARLY SARS-COV-2 TRANSMISSION IN SPAIN

2020 ◽  
Author(s):  
Francisco Díez-Fuertes ◽  
María Iglesias-Caballero ◽  
Javier García Pérez ◽  
Sara Monzón ◽  
Pilar Jiménez ◽  
...  
Keyword(s):  
Founder Effect ◽  
Phylogenetic Analyses ◽  
Protein A ◽  
Spike Protein ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Most Recent Common Ancestor ◽  
Fitness Advantage

SARS-CoV-2 whole-genome analysis has identified five large clades worldwide, emerged in 2019 (19A and 19B) and in 2020 (20A, 20B and 20C). This study aims to analyze the diffusion of SARS-CoV-2 in Spain using maximum likelihood phylogenetic and Bayesian phylodynamic analyses. The most recent common ancestor (MRCA) of the SARS-CoV-2 pandemic was estimated in Wuhan, China, around November 24, 2019. Phylogenetic analyses of the first 12,511 SARS-CoV-2 whole genome sequences obtained worldwide, including 290 from 11 different regions of Spain, revealed 62 independent introductions of the virus in the country. Most sequences from Spain were distributed in clades characterized by D614G substitution in S gene (20A, 20B and 20C) and L84S substitution in ORF8 (19B) with 163 and 118 sequences, respectively, with the remaining sequences branching in 19A. A total of 110 (38%) sequences from Spain grouped in four different monophyletic clusters of 20A clade (20A-Sp1 and 20A-Sp2) and 19B clade (19B-Sp1 and 19B-Sp2) along with sequences from 29 countries worldwide. The MRCA of 19A-Sp1, 20A-Sp1, 19A-Sp2 and 20A-Sp2 clusters were estimated in Spain around January 21 and 29, and February 6 and 17, 2020, respectively. The prevalence of 19B clade in Spain (40%) was by far higher than in any other European country during the first weeks of the epidemic, probably by a founder effect. However, this variant was replaced by G614-bearing viruses in April. In vitro assays showed an enhanced infectivity of pseudotyped virions displaying G614 substitution compared with D614, suggesting a fitness advantage of D614G. IMPORTANCE Multiple SARS-CoV-2 introductions have been detected in Spain and at least four resulted in the emergence of locally transmitted clusters originated not later than mid-February, with further dissemination to many other countries around the world and a few weeks before the explosion of COVID-19 cases detected in Spain during the first week of March. The majority of the earliest variants detected in Spain branched in 19B clade (D614 viruses), which was the most prevalent clade during the first weeks of March, pointing to a founder effect. However, from mid-March to June, 2020, G614-bearing viruses (20A, 20B and 20C clades) overcame D614 variants in Spain, probably as a consequence of an evolutionary advantage of this substitution in the spike protein. A higher infectivity of G614-bearing viruses compared to D614 variants was detected, suggesting that this substitution in SARS-CoV-2 spike protein could be behind the variant shift observed in Spain.

scholarly journals Phylogenetic Relationships Within the Family Potyviridae: Wheat Streak Mosaic Virus and Brome Streak Mosaic Virus Are Not Members of the Genus Rymovirus

1998 ◽  
Vol 88 (8) ◽  
pp. 782-787 ◽  
Author(s):  
Drake C. Stenger ◽  
Jeffrey S. Hall ◽  
Il-Ryong Choi ◽  
Roy French
Keyword(s):  
Mosaic Virus ◽  
Type Species ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Wheat Streak Mosaic Virus ◽  
Recent Common Ancestor ◽  
Amino Acid Residues ◽  
Most Recent Common Ancestor ◽  
The Family ◽  
Eriophyid Mites

The complete nucleotide sequence of wheat streak mosaic virus (WSMV) has been determined based on complementary DNA clones derived from the 9,384-nucleotide (nt) RNA of the virus. The genome of WSMV has a 130-nt 5′ leader and 149-nt 3′-untranslated region and is polyadenylated at the 3′ end. WSMV RNA encodes a single polyprotein of 3,035 amino acid residues and has a deduced genome organization typical for a member of the family Potyviridae (5′-P1/HC-Pro/P3/6K1/CI/6K2/VPg-NIa/NIb/CP-3′). Because WSMV shares with ryegrass mosaic virus (RGMV) the biological property of transmission by eriophyid mites, WSMV has been assigned to the genus Rymovirus, of which RGMV is the type species. Phylogenetic analyses were conducted with complete polyprotein or NIb protein sequences of 11 members of the family Potyviridae, including viruses of monocots or dicots and viruses transmitted by aphids, whiteflies, and mites. WSMV and the monocot-infecting, mite-transmitted brome streak mosaic virus (BrSMV) are sister taxa and share a most recent common ancestor with the whitefly-transmitted sweet potato mild mottle virus, the type species of the proposed genus “Ipomovirus.” In contrast, RGMV shares a most recent common ancestor with aphid-transmitted species of the genus Potyvirus. These results indicate that WSMV and BrSMV should be classified within a new genus of the family Potyviridae and should not be considered species of the genus Rymovirus.

scholarly journals Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia

2021 ◽  
Vol 9 ◽  
Author(s):  
Mingjian Zhu ◽  
Jian Shen ◽  
Qianli Zeng ◽  
Joanna Weihui Tan ◽  
Jirapat Kleepbua ◽  
...  
Keyword(s):  
Southeast Asia ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Population Expansion ◽  
Principal Component ◽  
Viral Population ◽  
Recent Common Ancestor ◽  
Tropical Region ◽  
Effective Population ◽  
Most Recent Common Ancestor

Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region.Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model.Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10−3 (1.292 × 10−3 to 1.613 × 10−3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia.Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.

scholarly journals Phylogenetic relationships, origin and historical biogeography of the genus Sprattus (Clupeiformes: Clupeidae)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11737
Author(s):  
Cristian B. Canales-Aguirre ◽  
Peter A. Ritchie ◽  
Sebastián Hernández ◽  
Victoria Herrera-Yañez ◽  
Sandra Ferrada Fuentes ◽  
...  
Keyword(s):  
Southern Hemisphere ◽  
Northern Hemisphere ◽  
Dna Sequences ◽  
Phylogenetic Analyses ◽  
Historical Biogeography ◽  
Ancestral Population ◽  
Recent Common Ancestor ◽  
Most Recent Common Ancestor ◽  
The Tropics ◽  
Two Populations

The genus Sprattus comprises five species of marine pelagic fishes distributed worldwide in antitropical, temperate waters. Their distribution suggests an ancient origin during a cold period of the earth’s history. In this study, we evaluated this hypothesis and corroborated the non-monophyly of the genus Sprattus, using a phylogenetic approach based on DNA sequences of five mitochondrial genome regions. Sprattus sprattus is more closely related to members of the genus Clupea than to other Sprattus species. We also investigated the historical biogeography of the genus, with the phylogenetic tree showing two well-supported clades corresponding to the species distribution in each hemisphere. Time-calibrated phylogenetic analyses showed that an ancient divergence between Northern and Southern Hemispheres occurred at 55.8 MYBP, followed by a diversification in the Oligocene epoch in the Northern Hemisphere clade (33.8 MYBP) and a more recent diversification in the Southern Hemisphere clade (34.2 MYBP). Historical biogeography analyses indicated that the most recent common ancestor (MRCA) likely inhabited the Atlantic Ocean in the Southern Hemisphere. These results suggest that the ancestral population of the MRCA diverged in two populations, one was dispersed to the Northern Hemisphere and the other across the Southern Hemisphere. Given that the Eocene was the warmest epoch since the Paleogene, the ancestral populations would have crossed the tropics through deeper cooler waters, as proposed by the isothermal submergence hypothesis. The non-monophyly confirmed for the genus Sprattus indicates that its systematics should be re-evaluated.

scholarly journals The evolutionary history of Stomatopoda (Crustacea: Malacostraca) inferred from molecular data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3844 ◽  
Author(s):  
Cara Van Der Wal ◽  
Shane T. Ahyong ◽  
Simon Y.W. Ho ◽  
Nathan Lo
Keyword(s):  
Phylogenetic Analyses ◽  
Sister Group ◽  
Molecular Data ◽  
Recent Common Ancestor ◽  
Ancestral State ◽  
Crown Group ◽  
Most Recent Common Ancestor ◽  
History Of ◽  
The Tropics ◽  
Age Constraints

The crustacean order Stomatopoda comprises seven superfamilies of mantis shrimps, found in coastal waters of the tropics and subtropics. These marine carnivores bear notable raptorial appendages for smashing or spearing prey. We investigated the evolutionary relationships among stomatopods using phylogenetic analyses of three mitochondrial and two nuclear markers. Our analyses recovered the superfamily Gonodactyloidea as polyphyletic, withHemisquillaas the sister group to all other extant stomatopods. A relaxed molecular clock, calibrated by seven fossil-based age constraints, was used to date the origin and major diversification events of stomatopods. Our estimates suggest that crown-group stomatopods (Unipeltata) diverged from their closest crustacean relatives about 340 Ma (95% CRI [401–313 Ma]). We found that the specialized smashing appendage arose after the spearing appendage ∼126 Ma (95% CRI [174–87 Ma]). Ancestral state reconstructions revealed that the most recent common ancestor of extant stomatopods had eyes with six midband rows of hexagonal ommatidia. Hexagonal ommatidia are interpreted as plesiomorphic in stomatopods, and this is consistent with the malacostracan ground-plan. Our study provides insight into the evolutionary timescale and systematics of Stomatopoda, although further work is required to resolve with confidence the phylogenetic relationships among its superfamilies.

scholarly journals Predominance of hepatitis C virus genotype 4 infection and rapid transmission between 1935 and 1965 in the Central African Republic

2009 ◽  
Vol 90 (10) ◽  
pp. 2452-2456 ◽  
Author(s):  
Richard Njouom ◽  
Eric Frost ◽  
Sylvie Deslandes ◽  
Fleurie Mamadou-Yaya ◽  
Annie-Claude Labbé ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Central African Republic ◽  
Phylogenetic Analyses ◽  
Recent Common Ancestor ◽  
Evolutionary Analysis ◽  
Virus Genotype ◽  
Genotype 4 ◽  
Most Recent Common Ancestor ◽  
Genotype 2

The molecular epidemiology of hepatitis C virus (HCV) in the Central African Republic (CAR) is poorly documented. Thus, we conducted phylogenetic analyses of NS5B gene sequences from 58 HCV-infected inhabitants of a remote area of south-west CAR, which indicated that 48 (82.8 %) were infected with genotype 4 (HCV-4), five (8.6 %) with genotype 2 and five (8.6 %) with genotype 1. HCV-4 strains were highly heterogeneous, containing previously described subtypes 4k (48 %), 4c (27 %), 4r (4 %), 4f (4 %) and unclassified subtypes (17 %). To estimate the epidemic history of these HCV-4 strains, an evolutionary analysis using the coalescent approach was used. The estimated date of the most recent common ancestor of the CAR HCV-4 strains was 1539 (95 % confidence intervals, 1317–1697). They exhibited a rapid, exponential spread from 1935 to 1965, simultaneously with what was recently reported in neighbouring Cameroon and Gabon. The hypothesis of a massive iatrogenic transmission during interventions for the control of endemic tropical diseases is discussed.

scholarly journals Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 93
Author(s):  
Javier E. Cañada ◽  
Elena Delgado ◽  
Horacio Gil ◽  
Mónica Sánchez ◽  
Sonia Benito ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Basque Country ◽  
Recent Common Ancestor ◽  
Subtype C ◽  
Northern Spain ◽  
Most Recent Common Ancestor ◽  
Phylogenetic Cluster ◽  
Subtype B ◽  
Definition Of ◽  
Hiv 1

The extraordinary genetic variability of human immunodeficiency virus type 1 (HIV-1) group M has led to the identification of 10 subtypes, 102 circulating recombinant forms (CRFs) and numerous unique recombinant forms. Among CRFs, 11 derived from subtypes B and C have been identified in China, Brazil, and Italy. Here we identify a new HIV-1 CRF_BC in Northern Spain. Originally, a phylogenetic cluster of 15 viruses of subtype C in protease-reverse transcriptase was identified in an HIV-1 molecular surveillance study in Spain, most of them from individuals from the Basque Country and heterosexually transmitted. Analyses of near full-length genome sequences from six viruses from three cities revealed that they were BC recombinant with coincident mosaic structures different from known CRFs. This allowed the definition of a new HIV-1 CRF designated CRF108_BC, whose genome is predominantly of subtype C, with four short subtype B fragments. Phylogenetic analyses with database sequences supported a Brazilian ancestry of the parental subtype C strain. Coalescent Bayesian analyses estimated the most recent common ancestor of CRF108_BC in the city of Vitoria, Basque Country, around 2000. CRF108_BC is the first CRF_BC identified in Spain and the second in Europe, after CRF60_BC, both phylogenetically related to Brazilian subtype C strains.

scholarly journals Evolutionary dynamics of GII.17 norovirus

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4333 ◽  
Author(s):  
Shaowei Sang ◽  
Xiaoyun Yang
Keyword(s):  
Binding Site ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Recent Common Ancestor ◽  
Blood Group Antigens ◽  
The Novel ◽  
Nucleotide Substitutions ◽  
Most Recent Common Ancestor ◽  
Likelihood Analysis ◽  
Amino Acid Distance

Background During the winter of 2014–2015, a rarely reported norovirus (NoV) genotype GII.17 was found to have increased its frequency in norovirus outbreaks in East Asia, surpassing the GII.4 NoV infections. GII.17 genotype has been detected for over three decades in the world. The aim of this study is to examine the evolutionary dynamics of GII.17 over the last four decades. Methods NoV GII.17 sequences with complete or nearly complete VP1 were downloaded from GenBank and the phylogenetic analyses were then conducted. Results The maximum likelihood analysis showed that GII.17 genotype could be divided into four different clades (Clades A–D). The strains detected after 2012, which could be the cause of the outbreaks, were separated into Clades C–D with their mean amino acid distance being 4.5%. Bayesian Markov chain Monte Carlo analyses indicated that the rate of nucleotide substitution per sites was 1.68 × 10−3 nucleotide substitutions/site/year and the time of the most recent common ancestor was 1840. The P2 subdomain of GII.17 was highly variable with 44% (56/128) amino acids variations including two insertions at positions 295–296 and one deletion at position 385 (Clades C and D) and one insertion at position 375 (Clade D). Variations existed in Epitopes A, B and D corresponding to GII.4 and human histo-blood group antigens binding site I in P2 subdomain. Conclusion The novel GII.17 strains that caused outbreaks in 2013–2015 may have two new variants. The evolvement of HBGAs binding site and epitopes in P2 subdomain might contribute to the novel GII.17 strains predominance in some regions.

scholarly journals An exploration of the complex biogeographical history of the Neotropical banner-wing damselflies (Odonata: Polythoridae)

2020 ◽  
Author(s):  
Melissa Sanchez Herrera ◽  
Christopher Beatty ◽  
Renato Nunes ◽  
Camilo Salazar ◽  
Jessica L Ware
Keyword(s):  
Amazon Basin ◽  
Late Eocene ◽  
Recent Common Ancestor ◽  
Northern Andes ◽  
Intrinsic Factors ◽  
Most Recent Common Ancestor ◽  
Early Diversification ◽  
Dynamic Landscape ◽  
History Of ◽  
Spatial Diversification

Abstract Background: The New World Tropics has experienced a dynamic landscape across evolutionary history and harbors a high diversity of flora and fauna. While there are some studies addressing diversification in Neotropical vertebrates and plants, there is still a lack of knowledge in arthropods. Here we examine temporal and spatial diversification patterns in the damselfly family Polythoridae, which comprises seven genera with a total of 58 species distributed across much of Central and South America. Results Our time-calibrated phylogeny for 48 species suggests that this family radiated during the late Eocene (~33 Ma), diversifying during the Miocene. As with other neotropical groups, the Most Recent Common Ancestor (MRCA) of most of the Polythoridae genera has a primary origin in the Northern Andes though the MRCA of at least one genus may have appeared in the Amazon Basin. Our molecular clock suggests correlations with some major geographical events, and our biogeographical modeling (with BioGeoBEARS and RASP) found a significant influence of the formation of the Pebas and Acre systems on the early diversification of these damselflies, though evidence for the influence of the rise of the different Andean ranges was mixed. Diversification rates have been uniform in all genera except one— Polythore —where a significant increase in the late Pliocene (~3 mya) may have been influenced by recent Andean uplift. Conclusion The biogeographical models implemented here suggest that the Pebas and Acre Systems were significant geological events associated with the diversification of this damselfly family; while diversification in the tree shows some correlation with mountain building events, it is possible that other abiotic and biotic changes during our study period have influenced diversification as well. The high diversification rate observed in Polythore could be explained by the late uplift of the Northern Andes. However, it is possible that other intrinsic factors like sexual and natural selection acting on color patterns could be involved in the diversification of this genus.

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