A Not-So-Long Introduction to Computational Molecular Evolution

Aris‐Brosou, Stéphane; Rodrigue, Nicolas

doi:10.1007/978-1-4939-9074-0_3

Cited by 4 publications

(3 citation statements)

References 213 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Alignments were then refined using trimAI (Capella-Gutiérrez et al, 2009 ) and the parameter. FastTree2 (Price et al, 2010 ), recompiled with double precision to resolve short branch lengths, was used to infer maximum likelihood phylogenetic trees from protein sequence alignments under the WAG +Γ model (Whelan and Goldman, 2001 ; Aris-Brosou and Rodrigue, 2012 , 2019 ). The archaeal tree was rooted with Euryarchaeota and the bacterial tree was rooted with Patescibacteria using the R package APE (Paradis et al, 2004 ).…”

Section: Methodsmentioning

confidence: 99%

Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake

et al. 2020

Self Cite

View full text Add to dashboard Cite

Temperatures in the Arctic are expected to increase dramatically over the next century, and transform high latitude watersheds. However, little is known about how microbial communities and their underlying metabolic processes will be affected by these environmental changes in freshwater sedimentary systems. To address this knowledge gap, we analyzed sediments from Lake Hazen, NU Canada. Here, we exploit the spatial heterogeneity created by varying runoff regimes across the watershed of this uniquely large high-latitude lake to test how a transition from low to high runoff, used as one proxy for climate change, affects the community structure and functional potential of dominant microbes. Based on metagenomic analyses of lake sediments along these spatial gradients, we show that increasing runoff leads to a decrease in taxonomic and functional diversity of sediment microbes. Our findings are likely to apply to other, smaller, glacierized watersheds typical of polar or high latitude ecosystems; we can predict that such changes will have far reaching consequences on these ecosystems by affecting nutrient biogeochemical cycling, the direction and magnitude of which are yet to be determined.

show abstract

Section: Methodsmentioning

confidence: 99%

Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake

et al. 2020

Self Cite

View full text Add to dashboard Cite

show abstract

“…FastTree ver. 2.1.1 (Price et al , 2010) was used to generate a first phylogenetic tree for each of the four datasets, assuming the General Time-Reversible +Γ model of evolution ( e.g., Aris-Brosou and Rodrigue, 2019). Sequences with extreme branch lengths were removed, leaving us with 5,288 HA and 9,331 NA sequences for H1N1, and 16,493 HA and 14,403 NA sequences for H3N2.…”

Section: Methodsmentioning

confidence: 99%

“…When many amino acids interact in such a way, they are considered to evolve in a correlated manner, often forming networks of coevolving residues (Nshogozabahizi et al , 2017), networks that are not limited to viruses as they are also found in bacteria (Dench et al , 2020). These networks are thought to stabilize a genome from an evolutionary point of view (Aris-Brosou et al , 2019), a stability that is compromised during an outbreak, potentially because of a lack of compensatory mutations. Because this previous work was limited to case studies, it remains unclear whether such associations can be generalized, and more critically how they translate in the clinic.…”

Section: Introductionmentioning

confidence: 99%

Viral evolutionary dynamics predict Influenza-Like-Illnesses in patients

Aris‐Brosou

2021

Preprint

Self Cite

View full text Add to dashboard Cite

While viral infections such as those cause by the influenza virus can put a strain on any healthcare system. However, such a burden is typically difficult to predict. In order to improve such predictions, we here leverage on recent work that showed the existence of an association between viral evolutionary dynamics and severe outbreaks in the case of select viruses such as Ebola in 2014-16, Zika in 2015-16, and of the 2009 pandemic influenza. As this previous work examined case studies, it remains unclear whether such associations can be generalized, and how they translate in the clinic. To address these issues, we performed a systematic survey of influenza viruses circulating in continental US between 2010 and 2019, hypothesizing that measures of the evolutionary dynamics of these viruses correlate with the severity of the epidemic with respect to clinical data based on outpatient healthcare visits showing Influenza-like illness symptoms. By reconstructing the networks of coevolving amino acids in the hemagglutinin and neuraminidase genes, we first show evidence of a significant correlation between viral evolutionary dynamics and increased influenza activity during seasonal epidemics, and then show that these dynamics closely follow the progression of epidemics through each season, providing us with predictive power based off genetic data collected between week 20 and week 40/52, i.e. one to fifteen weeks prior to peak ILI burden. This may leave enough time for health authorities to adjust their logistics.

show abstract

Deduction and exploration of the evolution and function of vertebrate GFPT family

Wei

et al. 2022

Genes Genom

View full text Add to dashboard Cite

A Not-So-Long Introduction to Computational Molecular Evolution

Cited by 4 publications

References 213 publications

Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake

Warming Climate Is Reducing the Diversity of Dominant Microbes in the Largest High Arctic Lake

Viral evolutionary dynamics predict Influenza-Like-Illnesses in patients

Deduction and exploration of the evolution and function of vertebrate GFPT family

Contact Info

Product

Resources

About