RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution DOI Creative Commons
Ruby Redlich, Amanda Kowalczyk,

Michael Tene

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 7, 2023

Abstract Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many these methods, including our rates based method, RERconverge, lack capability analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion RERconverge that associates shifts in convergent multi-categorical The categorical includes methods for performing ancestral state reconstruction, statistical tests associating relative variables, and new method phylogenetic permulations on In addition demonstrating three-category diet phenotype, compare its performance naive pairwise binary analyses two existing comparative genomic traits: simulations signal method. We also present diagnostic analysis approach how scales number species categories included analysis. Our results show outperforms at identifying genes enriched pathways significantly associated phenotype reconstruction drives improvement ability capture diet-related pathways. were able account non-uniform null distributions correct non-independence gene rank during pathway enrichment will provide strong foundation applying traits larger data sets more complex trait evolution.

Language: Английский

Revealing the comprehensive impact of organic compounds on the partial nitrification-anammox system during incineration leachate treatment: metabolic hierarchy and adaptation DOI

Mingda Zhou,

Junjie Wang, Han Wang

et al.

Water Research, Journal Year: 2024, Volume and Issue: 255, P. 121534 - 121534

Published: March 26, 2024

Language: Английский

Citations

8
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches DOI Creative Commons
Blox Bloxham, Hyunseok Lee, Jeff Gore

et al.

PLoS Computational Biology, Journal Year: 2024, Volume and Issue: 20(5), P. e1012049 - e1012049

Published: May 13, 2024

How natural communities maintain their remarkable biodiversity and which species survive in complex are central questions ecology. Resource competition models successfully explain many phenomena but typically predict only as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles support more than resources. We explore how modify own environments by sequentially depleting to form sequences of temporal niches, intermediately depleted environments. Biodiversity is enhanced when community-driven environmental fluctuations modulate the depletion order produce different niches on each cycle. Community-driven under constant conditions rare, exploring them illuminates niche structure emerges from utilization. With fluctuations, find most have stably coexisting survivors accurately predicted same following a distinct optimal strategy. Our results thus present new niche-based approach understanding highly diverse fluctuating communities.

Language: Английский

Citations

5
Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches DOI Creative Commons
Blox Bloxham, Hyunseok Lee, Jeff Gore

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Feb. 21, 2023

Abstract How natural communities maintain their remarkable biodiversity and which species survive in complex are central questions ecology. Resource competition models successfully explain many phenomena but typically predict only as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles support more than resources. We explore how modify own environments by sequentially depleting to form sequences of temporal niches, intermediately depleted environments. Biodiversity is enhanced when community-driven environmental fluctuations modulate the depletion order produce different niches on each cycle. Community-driven under constant conditions rare, exploring them illuminates niche structure emerges from utilization. With fluctuations, find most have stably coexisting survivors accurately predicted same following a distinct optimal strategy. Our results thus present new niche-based approach understanding highly diverse fluctuating communities.

Language: Английский

Citations

8
Metabolic similarity and the predictability of microbial community assembly DOI Creative Commons
Jean C. C. Vila, Joshua E. Goldford, Sylvie Estrela

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 28, 2023

When microbial communities form, their composition is shaped by selective pressures imposed the environment. Can we predict which will assemble under different environmental conditions? Here, hypothesize that quantitative similarities in metabolic traits across metabolically similar environments lead to predictable community composition. To end, measured growth rate and by-product profile of a library proteobacterial strains large number single nutrient environments. We found rates secretion profiles were positively correlated when supplied substrate was similar. By analyzing hundreds in-vitro experimentally assembled an array synthetic environments, then show substrates select for taxonomically communities. These findings us propose validate comparative approach quantitatively predicting effects novel on complex consortia.

Language: Английский

Citations

8
Highlight: Forging Cheaters in Iron-Limited Microbial Communities DOI Creative Commons
Casey McGrath

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(4)

Published: April 1, 2024

Language: Английский

Citations

1
RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution DOI Creative Commons
Ruby Redlich, Amanda Kowalczyk,

Michael Tene

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 7, 2023

Abstract Comparative genomics approaches seek to associate evolutionary genetic changes with the evolution of phenotypes across a phylogeny. Many these methods, including our rates based method, RERconverge, lack capability analyzing non-ordinal, multicategorical traits. To address this limitation, we introduce an expansion RERconverge that associates shifts in convergent multi-categorical The categorical includes methods for performing ancestral state reconstruction, statistical tests associating relative variables, and new method phylogenetic permulations on In addition demonstrating three-category diet phenotype, compare its performance naive pairwise binary analyses two existing comparative genomic traits: simulations signal method. We also present diagnostic analysis approach how scales number species categories included analysis. Our results show outperforms at identifying genes enriched pathways significantly associated phenotype reconstruction drives improvement ability capture diet-related pathways. were able account non-uniform null distributions correct non-independence gene rank during pathway enrichment will provide strong foundation applying traits larger data sets more complex trait evolution.

Language: Английский

Citations

2