scholarly journals Reticulate evolution is favored in influenza niche switching

2015 ◽  
Author(s):  
Eric J. Ma ◽  
Nichola J. Hill ◽  
Justin Zabilansky ◽  
Kyle Yuan ◽  
Jonathan A. Runstadler
Keyword(s):  
Host Species ◽  
Influenza A ◽  
Sequence Data ◽  
Quantitative Difference ◽  
Reticulate Evolution ◽  
Ecological Niches ◽  
Research Database ◽  
Evolutionary Processes ◽  
Host Switch ◽  
Sequencing Project

AbstractReticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in transmission between different host species. Moreover, as host evolutionary distance increases, reassortment is increasingly favored. We conclude that the greater the quantitative difference between ecological niches, the greater the importance of reticulate evolutionary processes in overcoming niche barriers.Significance StatementAre the processes that result in the exchange of genes between microbes quantitatively advantageous for those microbes when switching between ecological niches? To address this question, we consider the influenza A virus as a model microbe, with its ability to infect multiple host species (ecological niches) and undergo reassortment (exchange genes) with one another. Through our analysis of sequence data from the Influenza Research Database and the Barcode of Life Database, we find that the greater the quantitative difference between influenza hosts, the greater the proportion of reassortment events were found. More broadly, for microbes, we infer that reticulate evolutionary processes should be quantitatively favoured when switching between ecological niches.

scholarly journals Reticulate evolution is favored in influenza niche switching

2016 ◽  
Vol 113 (19) ◽  
pp. 5335-5339 ◽  
Author(s):  
Eric J. Ma ◽  
Nichola J. Hill ◽  
Justin Zabilansky ◽  
Kyle Yuan ◽  
Jonathan A. Runstadler
Keyword(s):  
Genome Sequencing ◽  
Quantitative Difference ◽  
Reticulate Evolution ◽  
Ecological Niches ◽  
Genome Sequencing Project ◽  
Adaptive Traits ◽  
Evolutionary Processes ◽  
Host Switch ◽  
Evolutionary Mechanism ◽  
Sequencing Project

Reticulate evolution is thought to accelerate the process of evolution beyond simple genetic drift and selection, helping to rapidly generate novel hybrids with combinations of adaptive traits. However, the long-standing dogma that reticulate evolutionary processes are likewise advantageous for switching ecological niches, as in microbial pathogen host switch events, has not been explicitly tested. We use data from the influenza genome sequencing project and a phylogenetic heuristic approach to show that reassortment, a reticulate evolutionary mechanism, predominates over mutational drift in transmission between different host species. Moreover, as host evolutionary distance increases, reassortment is increasingly favored. We conclude that the greater the quantitative difference between ecological niches, the greater the importance of reticulate evolutionary processes in overcoming niche barriers.

scholarly journals Improving pandemic influenza risk assessment

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Colin A Russell ◽  
Peter M Kasson ◽  
Ruben O Donis ◽  
Steven Riley ◽  
John Dunbar ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Sequence Data ◽  
Virus Genome ◽  
Influenza Viruses ◽  
Influenza Surveillance ◽  
Human Influenza ◽  
Influenza A Viruses ◽  
Virus Genotype

Assessing the pandemic risk posed by specific non-human influenza A viruses is an important goal in public health research. As influenza virus genome sequencing becomes cheaper, faster, and more readily available, the ability to predict pandemic potential from sequence data could transform pandemic influenza risk assessment capabilities. However, the complexities of the relationships between virus genotype and phenotype make such predictions extremely difficult. The integration of experimental work, computational tool development, and analysis of evolutionary pathways, together with refinements to influenza surveillance, has the potential to transform our ability to assess the risks posed to humans by non-human influenza viruses and lead to improved pandemic preparedness and response.

Genetic variation in the mitochondrial cytochrome c oxidase subunit 1 within Progamotaenia festiva (Cestoda: Anoplocephalidae) from macropodid marsupials

Parasitology ◽  
2007 ◽  
Vol 134 (10) ◽  
pp. 1465-1476 ◽  
Author(s):  
I. BEVERIDGE ◽  
S. SHAMSI ◽  
M. HU ◽  
N. B. CHILTON ◽  
R. B. GASSER
Keyword(s):  
Genetic Variation ◽  
Host Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Enzyme Electrophoresis ◽  
Single Strand Conformational Polymorphism ◽  
Oxidase Subunit ◽  
Single Host ◽  
Distinct Sequence ◽  
Sequence Types

SUMMARYGenetic variation was examined in the anoplocephalid cestode Progamotaenia festiva, from Australian marsupials, in order to test the hypothesis that P. festiva, is a complex of sibling species and to assess the extent of host switching reported previously based on multilocus enzyme electrophoresis (MEE). Polymerase chain reaction (PCR)-based single-strand conformational polymorphism (SSCP) was used for the analysis of sequence variation in the cytochrome c oxidase subunit 1 (cox1) gene among 179 specimens of P. festiva (identified based on morphology and predilection site in the host) from 13 different host species, followed by selective DNA sequencing. Fifty-three distinct sequence types (haplotypes) representing all specimens were defined. Phylogenetic analyses of these sequence data (utilizing maximum parsimony and neighbour-joining methods) revealed 12 distinct clades. Other heterologous species, P. ewersi and P. macropodis, were used as outgroups and the remaining bile-duct inhabiting species, P. diaphana and P. effigia, were included in the analysis for comparative purposes. The latter 2 species were nested within the clades representing P. festiva. Most clades of P. festiva identified were restricted to a single host species; one clade primarily in Macropus robustus was also found in the related host species M. antilopinus in an area of host sympatry; another clade occurring primarily in M. robustus occurred also in additional kangaroo species, M. rufus and M. dorsalis. High levels of genetic divergence, the existence of distinct clades and their occurrence in sympatry provide support for the hypothesis that P. festiva represents a complex of numerous species, most of which, but not all, are host specific. Three distinct clades of cestodes were found within a single host, M. robustus, but there was no evidence of within-host speciation.

Codon usage characteristics of PB2 gene in influenza A H7N9 virus from different host species

2018 ◽  
Vol 65 ◽  
pp. 430-435 ◽  
Author(s):  
Li Gun ◽  
Pan Haixian ◽  
Ren Yumiao ◽  
Tian Han ◽  
Lu Jingqi ◽  
...  
Keyword(s):  
Codon Usage ◽  
Host Species ◽  
Influenza A ◽  
H7n9 Virus

scholarly journals Multi-gene incongruence consistent with hybridisation in Cladocopium (Symbiodiniaceae), an ecologically important genus of coral reef symbionts

2019 ◽  
Author(s):  
Joshua I Brian ◽  
Simon K Davy ◽  
Shaun P Wilkinson
Keyword(s):  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Reticulate Evolution ◽  
Next Generation Sequencing Data ◽  
Putative Hybrid ◽  
Its2 Region ◽  
Sequencing Data ◽  
Lineage Sorting ◽  
Evolutionary Potential ◽  
Unbiased Test

Coral reefs rely on their intracellular dinoflagellate symbionts (family Symbiodiniaceae) for nutritional provision in nutrient-poor waters, yet this association is threatened by thermally stressful conditions. Despite this, the evolutionary potential of these symbionts remains poorly characterised. In this study, we tested the potential for divergent Symbiodiniaceae types to sexually reproduce (i.e. hybridise) within Cladocopium, the most ecologically prevalent genus in this family. With sequence data from three organelles (cob gene, mitochondria; psbAncr region, chloroplast; and ITS2 region, nucleus), we utilised the Incongruence Length Difference test, Approximately Unbiased test, tree hybridisation analyses and visual inspection of raw data in stepwise fashion to highlight incongruences between organelles, and thus provide evidence of reticulate evolution. Using this approach, we identified three putative hybrid Cladocopium samples among the 158 analysed, at two of the seven sites sampled. These samples were identified as the common Cladocopium types C40 or C1 with respect to the mitochondria and chloroplasts, but the rarer types C3z, C3u and C1# with respect to their nuclear identity. These five Cladocopium types have previously been confirmed as evolutionarily distinct and were also recovered in non-incongruent samples multiple times, which is strongly suggestive that they sexually reproduced to produce the incongruent samples. A concomitant inspection of Next Generation Sequencing data for these samples suggests that other plausible explanations, such as incomplete lineage sorting, are much less likely. The approach taken in this study allows incongruences between gene regions to be identified with confidence, and brings new light to the evolutionary potential within Symbiodiniaceae.

Species delimitation of Hymenasplenium obliquissimum group (Aspleniaceae) in southwestern China

Phytotaxa ◽  
2021 ◽  
Vol 480 (1) ◽  
pp. 29-44
Author(s):  
GUO-CHENG ZHANG ◽  
HUA-FENG HONG ◽  
GE-HONG CHEN ◽  
SHU-GANG LU ◽  
YAN-FEN CHANG
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Reticulate Evolution ◽  
Southwestern China ◽  
Natural Classification ◽  
Ploidy Levels ◽  
Dna Sequence Data ◽  
Taxonomic Implications ◽  
Taxonomic Approach ◽  
Locus Classicus

The Hymenasplenium obliquissimum group contains the widespread H. obliquissimum and several geographically restricted species, including H. retusulum, H. wuliangshanense, H. latidens, H. changputungense, H. quercicola, H. szechuanense, H. furfuraceum, H. adiantifrons, and H. filipes. However, the taxonomy of this group is still unclear and needs to be revised because some entities were treated infraspecifically or as synonyms and the validation of some species still needs to be assessed. To formulate a natural classification and investigate the relationships in this group, we collected and studied specimens of species related to the H. obliquissimum group and obtained specimens of species described by Ching at their locus classicus in southwestern China. An integrative taxonomic approach was taken to delimit species in the group using cytological, morphological, and DNA sequence data. Specifically, in the phylogenetic analyses, the H. obliquissimum group was recovered as a monophyletic group, comprising five principal chloroplast lineages. Based on our inferences, we provided taxonomic implications of chloroplast lineages discovered in this study and suggested possible reticulate evolution in the H. obliquissimum group which was interpreted by the incongruence of chloroplast and nuclear phylogenies. Further studies to strengthen the taxonomic of taxa especially those with the co-existence of different ploidy levels are still warranted.

Biology of pathogenic microorganisms

2020 ◽  
pp. 651-656
Author(s):  
Duncan J. Maskell ◽  
James L.N. Wood
Keyword(s):  
Gene Expression ◽  
Ecological Niche ◽  
Rich Source ◽  
Ecological Niches ◽  
Pathogenic Microorganisms ◽  
Evolutionary Processes ◽  
Host Animal ◽  
Host Environment ◽  
The Rich

Microorganisms are present at most imaginable sites on the planet, and have evolved to occupy these ecological niches successfully. A host animal is simply another ecological niche to be occupied. This chapter describes how the ability to cause disease may in some cases be an accidental bystander event, or it may be the result of evolutionary processes that have led to specific mechanisms allowing the pathogen to exploit the rich source of nutrients present in the host, and then be transmitted to another fresh host. Pathogenicity often relies on a series of steps, with specific and often distinct mechanisms operating at each of them. Some types of pathogen must adapt to the host environment by altering gene expression, and most must retain the ability to be transmitted readily between hosts.

scholarly journals Use of a Mycobacterium tuberculosisH37Rv Bacterial Artificial Chromosome Library for Genome Mapping, Sequencing, and Comparative Genomics

1998 ◽  
Vol 66 (5) ◽  
pp. 2221-2229 ◽  
Author(s):  
Roland Brosch ◽  
Stephen V. Gordon ◽  
Alain Billault ◽  
Thierry Garnier ◽  
Karin Eiglmeier ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Bacterial Artificial Chromosome ◽  
Genome Mapping ◽  
Sequence Data ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Excellent Correlation ◽  
Sequencing Project ◽  
Polysaccharide Biosynthesis ◽  
Bac Clones

ABSTRACT The bacterial artificial chromosome (BAC) cloning system is capable of stably propagating large, complex DNA inserts in Escherichia coli. As part of the Mycobacterium tuberculosis H37Rv genome sequencing project, a BAC library was constructed in the pBeloBAC11 vector and used for genome mapping, confirmation of sequence assembly, and sequencing. The library contains about 5,000 BAC clones, with inserts ranging in size from 25 to 104 kb, representing theoretically a 70-fold coverage of the M. tuberculosisgenome (4.4 Mb). A total of 840 sequences from the T7 and SP6 termini of 420 BACs were determined and compared to those of a partial genomic database. These sequences showed excellent correlation between the estimated sizes and positions of the BAC clones and the sizes and positions of previously sequenced cosmids and the resulting contigs. Many BAC clones represent linking clones between sequenced cosmids, allowing full coverage of the H37Rv chromosome, and they are now being shotgun sequenced in the framework of the H37Rv sequencing project. Also, no chimeric, deleted, or rearranged BAC clones were detected, which was of major importance for the correct mapping and assembly of the H37Rv sequence. The minimal overlapping set contains 68 unique BAC clones and spans the whole H37Rv chromosome with the exception of a single gap of ∼150 kb. As a postgenomic application, the canonical BAC set was used in a comparative study to reveal chromosomal polymorphisms between M. tuberculosis, M. bovis, and M. bovis BCG Pasteur, and a novel 12.7-kb segment present in M. tuberculosis but absent from M. bovis and M. bovis BCG was characterized. This region contains a set of genes whose products show low similarity to proteins involved in polysaccharide biosynthesis. The H37Rv BAC library therefore provides us with a powerful tool both for the generation and confirmation of sequence data as well as for comparative genomics and other postgenomic applications. It represents a major resource for present and future M. tuberculosis research projects.

scholarly journals Trade-offs between and within scales: environmental persistence and within-host fitness of avian influenza viruses

2014 ◽  
Vol 281 (1787) ◽  
pp. 20133051 ◽  
Author(s):  
Andreas Handel ◽  
Camille Lebarbenchon ◽  
David Stallknecht ◽  
Pejman Rohani
Keyword(s):  
Avian Influenza ◽  
Influenza A ◽  
Influenza Viruses ◽  
Viral Fitness ◽  
Ecological Niches ◽  
Influenza A Viruses ◽  
Temperature Dependent ◽  
Environmental Persistence ◽  
Trade Off ◽  
Trade Offs

Trade-offs between different components of a pathogen's replication and transmission cycle are thought to be common. A number of studies have identified trade-offs that emerge across scales, reflecting the tension between strategies that optimize within-host proliferation and large-scale population spread. Most of these studies are theoretical in nature, with direct experimental tests of such cross-scale trade-offs still rare. Here, we report an analysis of avian influenza A viruses across scales, focusing on the phenotype of temperature-dependent viral persistence. Taking advantage of a unique dataset that reports both environmental virus decay rates and strain-specific viral kinetics from duck challenge experiments, we show that the temperature-dependent environmental decay rate of a strain does not impact within-host virus load. Hence, for this phenotype, the scales of within-host infection dynamics and between-host environmental persistence do not seem to interact: viral fitness may be optimized on each scale without cross-scale trade-offs. Instead, we confirm the existence of a temperature-dependent persistence trade-off on a single scale, with some strains favouring environmental persistence in water at low temperatures while others reduce sensitivity to increasing temperatures. We show that this temperature-dependent trade-off is a robust phenomenon and does not depend on the details of data analysis. Our findings suggest that viruses might employ different environmental persistence strategies, which facilitates the coexistence of diverse strains in ecological niches. We conclude that a better understanding of the transmission and evolutionary dynamics of influenza A viruses probably requires empirical information regarding both within-host dynamics and environmental traits, integrated within a combined ecological and within-host framework.

scholarly journals The Role of Reticulate Evolution in Creating Innovation and Complexity

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Kristen S. Swithers ◽  
Shannon M. Soucy ◽  
J. Peter Gogarten
Keyword(s):  
Metabolic Pathways ◽  
Driving Forces ◽  
Reticulate Evolution ◽  
Neutral Evolution ◽  
Ecological Niches ◽  
Eukaryotic Evolution ◽  
New Host ◽  
Whole Genome Duplications ◽  
Genome Duplications

Reticulate evolution encompasses processes that conflict with traditional Tree of Life efforts. These processes, horizontal gene transfer (HGT), gene and whole-genome duplications through allopolyploidization, are some of the main driving forces for generating innovation and complexity. HGT has a profound impact on prokaryotic and eukaryotic evolution. HGTs can lead to the invention of new metabolic pathways and the expansion and enhancement of previously existing pathways. It allows for organismal adaptation into new ecological niches and new host ranges. Although many HGTs appear to be selected for because they provide some benefit to their recipient lineage, other HGTs may be maintained by chance through random genetic drift. Moreover, some HGTs that may initially seem parasitic in nature can cause complexity to arise through pathways of neutral evolution. Another mechanism for generating innovation and complexity, occurring more frequently in eukaryotes than in prokaryotes, is gene and genome duplications, which often occur through allopolyploidizations. We discuss how these different evolutionary processes contribute to generating innovation and complexity.

Sign in / Sign up

Export Citation Format

Share Document