The mitogenome of Phytophthora agathidicida: Evidence for a not so recent arrival of the “kauri killing” Phytophthora in New Zealand

Phytophthora agathidicida is associated with a root rot that threatens the long-term survival of the iconic New Zealand kauri. Although it is widely assumed that this pathogen arrived in New Zealand post-1945, this hypothesis has yet to be formally tested. Here we describe evolutionary analyses aimed at evaluating this and two alternative hypotheses. As a basis for our analyses, we assembled complete mitochondrial genome sequences from 16 accessions representing the geographic range of P. agathidicida as well as those of five other members of Phytophthora clade 5. All 21 mitogenome sequences were very similar, differing little in size with all sharing the same gene content and arrangement. We first examined the temporal origins of genetic diversity using a pair of calibration schemes. Both resulted in similar age estimates; specifically, a mean age of 303.0–304.4 years and 95% HPDs of 206.9–414.6 years for the most recent common ancestor of the included isolates. We then used phylogenetic tree building and network analyses to investigate the geographic distribution of the genetic diversity. Four geographically distinct genetic groups were recognised within P. agathidicida. Taken together the inferred age and geographic distribution of the sampled mitogenome diversity suggests that this pathogen diversified following arrival in New Zealand several hundred to several thousand years ago. This conclusion is consistent with the emergence of kauri dieback disease being a consequence of recent changes in the relationship between the pathogen, host, and environment rather than a post-1945 introduction of the causal pathogen into New Zealand.

Download Full-text

Evolution and Genetic Diversity of Porcine Circovirus 3 in China

Viruses ◽

10.3390/v11090786 ◽

2019 ◽

Vol 11 (9) ◽

pp. 786 ◽

Cited By ~ 3

Author(s):

Ye Chen ◽

Quanming Xu ◽

Hong Chen ◽

Xian Luo ◽

Qi Wu ◽

...

Keyword(s):

Genetic Diversity ◽

Eastern China ◽

Porcine Circovirus ◽

Recent Common Ancestor ◽

Fujian Province ◽

Tissue Samples ◽

Genetic Characteristics ◽

Most Recent Common Ancestor ◽

Porcine Circovirus 3 ◽

High Degree

The identification of a new circovirus (Porcine Circovirus 3, PCV3) has raised concern because its impact on swine health is not fully known. In Fujian Province in eastern China, even its circulating status and genetic characteristics are unclear. Here, we tested 127 tissue samples from swine from Fujian Province that presented respiratory symptoms. All of the PCV3 positive samples were negative for many other pathogens involved in respiratory diseases like PCV2, PRRSV, and CSFV, suggesting that PCV3 is potentially pathogenic. From phylogenetic analysis, PCV3 strains are divided into two main clades and five sub-clades; PCV3a-1, PCV3a-2, PCV3a-3, PCV3b-1, and PCV3b-2. Our identified strains belong to genotypes PCV3a-1, PCV3a-2, PCV3a-3, and PCV3b-2, indicating a high degree of genetic diversity of PCV3 in Fujian province until 2019. Interestingly, we found the time of the most recent common ancestor (tMRCA) of PCV3 was dated to the 1950s, and PCV3 has a similar evolutionary rate as PCV2 (the main epidemic genotypes PCV2b and PCV2d). In addition, positive selection sites N56D/S and S77T/N on the capsid gene are located on the PCV3 antigen epitope, indicating that PCV3 is gradually adaptive in swine. In summary, our results provide important insights into the epidemiology of PCV3.

Download Full-text

How old are bacterial pathogens?

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.0990 ◽

2016 ◽

Vol 283 (1836) ◽

pp. 20160990 ◽

Cited By ~ 23

Author(s):

Mark Achtman

Keyword(s):

Genetic Diversity ◽

Common Ancestor ◽

Bacterial Pathogens ◽

Recent Common Ancestor ◽

Evolutionary Divergence ◽

Bacterial Diseases ◽

Most Recent Common Ancestor ◽

Anatomically Modern Humans ◽

H Pylori ◽

Medical Bacteriology

Only few molecular studies have addressed the age of bacterial pathogens that infected humans before the beginnings of medical bacteriology, but these have provided dramatic insights. The global genetic diversity of Helicobacter pylori , which infects human stomachs, parallels that of its human host. The time to the most recent common ancestor (tMRCA) of these bacteria approximates that of anatomically modern humans, i.e. at least 100 000 years, after calibrating the evolutionary divergence within H. pylori against major ancient human migrations. Similarly, genomic reconstructions of Mycobacterium tuberculosis , the cause of tuberculosis, from ancient skeletons in South America and mummies in Hungary support estimates of less than 6000 years for the tMRCA of M. tuberculosis . Finally, modern global patterns of genetic diversity and ancient DNA studies indicate that during the last 5000 years plague caused by Yersinia pestis has spread globally on multiple occasions from China and Central Asia. Such tMRCA estimates provide only lower bounds on the ages of bacterial pathogens, and additional studies are needed for realistic upper bounds on how long humans and animals have suffered from bacterial diseases.

Download Full-text

Population genomics of Mycobacterium tuberculosis in the Inuit

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1507071112 ◽

2015 ◽

Vol 112 (44) ◽

pp. 13609-13614 ◽

Cited By ~ 49

Author(s):

Robyn S. Lee ◽

Nicolas Radomski ◽

Jean-Francois Proulx ◽

Ines Levade ◽

B. Jesse Shapiro ◽

...

Keyword(s):

Genetic Diversity ◽

Mycobacterium Tuberculosis ◽

Population Genomics ◽

Purifying Selection ◽

Synonymous Substitution ◽

Nonsynonymous Snps ◽

Recent Common Ancestor ◽

Nucleotide Polymorphisms ◽

Most Recent Common Ancestor ◽

Bacterial Genetic

Nunavik, Québec suffers from epidemic tuberculosis (TB), with an incidence 50-fold higher than the Canadian average. Molecular studies in this region have documented limited bacterial genetic diversity among Mycobacterium tuberculosis isolates, consistent with a founder strain and/or ongoing spread. We have used whole-genome sequencing on 163 M. tuberculosis isolates from 11 geographically isolated villages to provide a high-resolution portrait of bacterial genetic diversity in this setting. All isolates were lineage 4 (Euro-American), with two sublineages present (major, n = 153; minor, n = 10). Among major sublineage isolates, there was a median of 46 pairwise single-nucleotide polymorphisms (SNPs), and the most recent common ancestor (MRCA) was in the early 20th century. Pairs of isolates within a village had significantly fewer SNPs than pairs from different villages (median: 6 vs. 47, P < 0.00005), indicating that most transmission occurs within villages. There was an excess of nonsynonymous SNPs after the diversification of M. tuberculosis within Nunavik: The ratio of nonsynonymous to synonymous substitution rates (dN/dS) was 0.534 before the MRCA but 0.777 subsequently (P = 0.010). Nonsynonymous SNPs were detected across all gene categories, arguing against positive selection and toward genetic drift with relaxation of purifying selection. Supporting the latter possibility, 28 genes were partially or completely deleted since the MRCA, including genes previously reported to be essential for M. tuberculosis growth. Our findings indicate that the epidemiologic success of M. tuberculosis in this region is more likely due to an environment conducive to TB transmission than a particularly well-adapted strain.

Download Full-text

Phylogenetic origin of the Monotropoideae inferred from partial 28S ribosomal RNA gene sequences

Canadian Journal of Botany ◽

10.1139/b92-210 ◽

1992 ◽

Vol 70 (8) ◽

pp. 1703-1708 ◽

Cited By ~ 7

Author(s):

K. W. Cullings ◽

T. D. Bruns

Keyword(s):

Ribosomal Rna ◽

Recent Common Ancestor ◽

Gradual Transition ◽

Rrna Gene ◽

28S Rrna ◽

28S Rrna Gene ◽

Most Recent Common Ancestor ◽

Alternative Hypotheses ◽

Degree Of Confidence ◽

Phylogenetic Origin

Despite more than 100 years of detailed analysis of morphology and macromolecules, the phylogenetic origin of the Monotropoideae remains unclear. In this study partial sequences from the 28S rRNA gene were used to test two alternative hypotheses: (i) that the Monotropoideae share a most recent common ancestor with the Arbutoideae in the Ericaceae or (ii) that the Monotropoideae is the end result of a gradual transition from autotrophism to mycotrophic parasitism in the Pyrolaceae. Our results support the hypothesis that the Monotropoideae and the Arbutoideae are a monophyletic group and that the Monotropoideae should be included in the Ericaceae rather than the Pyrolaceae. The Monotropoid species Pleuricospora fimbriolata could not be placed within either the Monotropoideae or the Arbutoideae with any degree of confidence, leaving open the possibility that the Monotropoideae is polyphyletic. Key words: Monotropoideae, Ericaceae, 28S rRNA gene, PCR, molecular systematics.

Download Full-text

Evolutionary dynamics of human and avian metapneumoviruses

Journal of General Virology ◽

10.1099/vir.0.2008/006957-0 ◽

2008 ◽

Vol 89 (12) ◽

pp. 2933-2942 ◽

Cited By ~ 67

Author(s):

Miranda de Graaf ◽

Albert D. M. E. Osterhaus ◽

Ron A. M. Fouchier ◽

Edward C. Holmes

Keyword(s):

Genetic Diversity ◽

Evolutionary Dynamics ◽

Recent Common Ancestor ◽

Human Populations ◽

Population Bottlenecks ◽

Genetic Lineages ◽

The Past ◽

Most Recent Common Ancestor ◽

Large Sets ◽

Respiratory Tract Illnesses

Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A–D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations – A1, A2, B1 and B2 – of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic diversity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The sampled genetic diversity of HMPV was found to have arisen within the past 119–133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic diversity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection.

Download Full-text

Extensive genetic diversity of bat-borne polyomaviruses reveals inter-family host-switching events

10.1101/627158 ◽

2019 ◽

Author(s):

Zhizhou Tan ◽

Gabriel Gonzalez ◽

Jinliang Sheng ◽

Jianmin Wu ◽

Fuqiang Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Large Population ◽

Recent Common Ancestor ◽

Host Switching ◽

Evolutionary Divergence ◽

Dna Viruses ◽

Most Recent Common Ancestor ◽

Evolutionary Scheme ◽

Horseshoe Bat ◽

Horseshoe Bats

AbstractPolyomaviruses (PyVs) are small, double-stranded DNA tumor viruses carried by diverse vertebrates. PyVs have previously been considered highly host restricted in mammalian hosts, with host-switching events thought rare or nonexistent. Prior investigations have revealed short-range host-switching events of PyVs in two different African bat species within the horseshoe bat genusRhinolophus. Herein, we have conducted a systematic investigation of PyVs in 1,083 archived bat samples collected from five provinces across China, and identified 192 PyVs from 186 bats from 15 host species within 6 families (Rhinolophidae, Vespertilionidae, Hipposideridae, Emballonuridae, Miniopteridae and Pteropodidae) representing 28 newly-described PyVs, indicative of extensive genetic diversity of bat PyVs. Surprisingly, two PyVs were identified in multiple bat species from different families, and another PyV clustered phylogenetically with PyVs carried by bats from a different host family, indicative of three inter-family PyV host-switching events. The time to most recent common ancestor (tMRCA) of the three events was estimated at 0.02-11.6 million years ago (MYA), which is inconsistent with the estimated tMRCA of their respective bat hosts (36.3-66.7 MYA), and is most parsimoniously explained by host-switching events. PyVs identified from geographically separated Chinese horseshoe bat species in the present study showed close genetic identities, and clustered with each other and with PyVs from African horseshoe bats, allowing assessment of the effects of positive selection in VP1 within the horseshoe bat family Rhinolophidae. Correlation analysis indicated that co-evolution with their hosts contributed much more to evolutionary divergence of PyV than geographic distance. In conclusion, our findings provide the first evidence of inter-family host-switching events of PyV in mammals and challenge the prevailing evolutionary paradigm for strict host restriction of mammalian PyVs.Author summarySince the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered both genetically stable and highly host-restricted in their mammalian hosts. In this study, we have identified multiple cases of host-switching events of PyVs by large scale surveillance in diverse bat species collected in China. These host-switching events occurred between bat families living in the same colony, indicating that a large population with frequent contacts between different bat species may represent an ecological niche facilitating PyV host-switching. The cases studied involved members of bats from several families, including horseshoe bats, which were previously found to harbor a number of highly virulent viruses to both humans and domestic animals. Our findings have provided evidence that even highly host-specific DNA viruses can transmit between bats of different species and indicate an increased propensity for spillover events involving horseshoe bats. We propose an evolutionary scheme for bat-borne PyVs in which intra-host divergence and host-switching has generated the diverse PyVs in present day bats. This scheme provides a useful model to study the evolution of PyVs in other hosts and, potentially, the modeling of bat zoonoses and the transmission of other DNA viruses in other mammals, including humans.

Download Full-text

Ancient DNA from the extinct Haitian cave-rail ( Nesotrochis steganinos ) suggests a biogeographic connection between the Caribbean and Old World

Biology Letters ◽

10.1098/rsbl.2020.0760 ◽

2021 ◽

Vol 17 (3) ◽

Author(s):

Jessica A. Oswald ◽

Ryan S. Terrill ◽

Brian J. Stucky ◽

Michelle J. LeFebvre ◽

David W. Steadman ◽

...

Keyword(s):

Common Ancestor ◽

Complete Mitochondrial Genome ◽

Recent Common Ancestor ◽

Evolutionary Relationships ◽

Human Settlement ◽

Comprehensive Understanding ◽

The Holocene ◽

Most Recent Common Ancestor ◽

Extant Species ◽

The Caribbean

Worldwide decline in biodiversity during the Holocene has impeded a comprehensive understanding of pre-human biodiversity and biogeography. This is especially true on islands, because many recently extinct island taxa were morphologically unique, complicating assessment of their evolutionary relationships using morphology alone. The Caribbean remains an avian hotspot but was more diverse before human arrival in the Holocene. Among the recently extinct lineages is the enigmatic genus Nesotrochis, comprising three flightless species. Based on morphology, Nesotrochis has been considered an aberrant rail (Rallidae) or related to flufftails (Sarothruridae). We recovered a nearly complete mitochondrial genome of Nesotrochis steganinos from fossils, discovering that it is not a rallid but instead is sister to Sarothruridae, volant birds now restricted to Africa and New Guinea, and the recently extinct, flightless Aptornithidae of New Zealand. This result suggests a widespread or highly dispersive most recent common ancestor of the group. Prior to human settlement, the Caribbean avifauna had a far more cosmopolitan origin than is evident from extant species.

Download Full-text

Evolution and Genetic Diversity of SARSCoV-2 in Africa Using Whole Genome Sequences

10.1101/2020.07.27.222901 ◽

2020 ◽

Author(s):

Babatunde Olarenwaju Motayo ◽

Olukunle Oluwapamilerin Oluwasemowo ◽

Paul Akiniyi Akinduti ◽

Babatunde Adebiyi Olusola ◽

Olumide T Aerege ◽

...

Keyword(s):

Genetic Diversity ◽

Amino Acid ◽

Spike Protein ◽

Recent Common Ancestor ◽

Whole Genome ◽

Genome Sequences ◽

Protein Amino Acid ◽

Protein Variant ◽

Health Crisis ◽

Most Recent Common Ancestor

ABSTRACTThe ongoing SARSCoV-2 pandemic was introduced into Africa on 14th February 2020 and has rapidly spread across the continent causing severe public health crisis and mortality. We investigated the genetic diversity and evolution of this virus during the early outbreak months using whole genome sequences. We performed; recombination analysis against closely related CoV, Bayesian time scaled phylogeny and investigated spike protein amino acid mutations. Results from our analysis showed recombination signals between the AfrSARSCoV-2 sequences and reference sequences within the N and S genes. The evolutionary rate of the AfrSARSCoV-2 was 4.133 × 10−4 high posterior density HPD (4.132 × 10−4 to 4.134 × 10−4) substitutions/site/year. The time to most recent common ancestor TMRCA of the African strains was December 7th 2019. The AfrSARCoV-2 sequences diversified into two lineages A and B with B being more diverse with multiple sub-lineages confirmed by both maximum clade credibility MCC tree and PANGOLIN software. There was a high prevalence of the D614-G spike protein amino acid mutation (82.61%) among the African strains. Our study has revealed a rapidly diversifying viral population with the G614 spike protein variant dominating, we advocate for up scaling NGS sequencing platforms across Africa to enhance surveillance and aid control effort of SARSCoV-2 in Africa.

Download Full-text

Molecular Surveillance of HIV-1 Infection in Krasnoyarsk Region, Russia: Epidemiology, Phylodynamics and Phylogeography

Current HIV Research ◽

10.2174/1570162x17666190618155816 ◽

2019 ◽

Vol 17 (2) ◽

pp. 114-125 ◽

Cited By ~ 1

Author(s):

Dmitry Neshumaev ◽

Aleksey Lebedev ◽

Marina Malysheva ◽

Anatoly Boyko ◽

Sergey Skudarnov ◽

...

Keyword(s):

Genetic Diversity ◽

Temporal Dynamics ◽

Phylogenetic Reconstruction ◽

Viral Population ◽

Recent Common Ancestor ◽

Krasnoyarsk Region ◽

Most Recent Common Ancestor ◽

And Migration ◽

Viral Lineage ◽

Hiv 1

Background:The information about the dynamics of the viral population and migration events that affect the epidemic in different parts of the Russia is insufficient. Possibly, the huge size of the country and limited transport accessibility to certain territories may determine unique traits of the HIV-1 evolutionary history in different regions.Objective:The aim of this study was to explore the genetic diversity of HIV-1 in the Krasnoyarsk region and reconstruct spatial-temporal dynamics of the infection in the region.Methods:The demographic and virologic data from 281 HIV-infected individuals in Krasnoyarsk region collected during 2011-2016 were analyzed. The time to the most recent common ancestor, evolutionary rates, population growth, and ancestral geographic movements was estimated using Bayesian coalescent-based methods.Results:The study revealed moderate diversity of the HIV-1 subtypes found in the region, which included A6 (92.3%), CRF063_02A (4.3%), B (1.1%), and unique recombinants (2.5%). Phylogenetic reconstruction revealed that the A6 subtype was introduced into Krasnoyarsk region by one viral lineage, which arose around 1996.9 (1994.5-1999.5). The phylogeography analysis pointed to Krasnoyarsk city as the geographical center of the epidemic, which further spread to central neighboring districts of the region. At least two epidemic growth phases of subtype A6 were identified which included exponential growth in early-2000s followed by the decline in the mid/late 2010s.Conclusion:This study demonstrates a change in the genetic diversity of HIV-1 in the Krasnoyarsk region. At the beginning of the epidemic, subtype A6 prevailed, subtypes B and CRF063_02A appeared in the region later.

Download Full-text

Genomic Epidemiology of SARS-CoV-2 From Mainland China With Newly Obtained Genomes From Henan Province

Frontiers in Microbiology ◽

10.3389/fmicb.2021.673855 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ning Song ◽

Guang-Lin Cui ◽

Qing-Lei Zeng

Keyword(s):

Genetic Diversity ◽

Molecular Epidemiology ◽

Mainland China ◽

Henan Province ◽

Whole Genome Sequence ◽

Recent Common Ancestor ◽

Whole Genome ◽

Genome Sequences ◽

Worst Case ◽

Most Recent Common Ancestor

Even though the COVID-19 epidemic in China has been successfully put under control within a few months, it is still very important to infer the origin time and genetic diversity from the perspective of the whole genome sequence of its agent, SARS-CoV-2. Yet, the sequence of the entire virus genome from China in the current public database is very unevenly distributed with reference to time and place of collection. In particular, only one sequence was obtained in Henan province, adjacent to China's worst-case province, Hubei Province. Herein, we used high-throughput sequencing techniques to get 19 whole-genome sequences of SARS-CoV-2 from 18 severe patients admitted to the First Affiliated Hospital of Zhengzhou University, a provincial designated hospital for the treatment of severe COVID-19 cases in Henan province. The demographic, baseline, and clinical characteristics of these patients were described. To investigate the molecular epidemiology of SARS-CoV-2 of the current COVID-19 outbreak in China, 729 genome sequences (including 19 sequences from this study) sampled from Mainland China were analyzed with state-of-the-art comprehensive methods, including likelihood-mapping, split network, ML phylogenetic, and Bayesian time-scaled phylogenetic analyses. We estimated that the evolutionary rate and the time to the most recent common ancestor (TMRCA) of SARS-CoV-2 from Mainland China were 9.25 × 10−4 substitutions per site per year (95% BCI: 6.75 × 10−4 to 1.28 × 10−3) and October 1, 2019 (95% BCI: August 22, 2019 to November 6, 2019), respectively. Our results contribute to studying the molecular epidemiology and genetic diversity of SARS-CoV-2 over time in Mainland China.

Download Full-text