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

Michael Tene

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(11)

Published: Oct. 15, 2024

Comparative genomics approaches seek to associate molecular evolution with the of phenotypes across a phylogeny. Many these methods lack ability analyze non-ordinal categorical traits more than two categories. To address this limitation, we introduce an expansion RERconverge that associates shifts in evolutionary rates convergent traits. The includes for performing ancestral state reconstruction, statistical tests associating relative variables, and new method phylogeny-aware permutations, "permulations", on We demonstrate our three-category diet phenotype, compare its performance binary analyses existing comparative genomic traits: phylogenetic simulations signal based method. present analysis how permulations scale number species categories included analysis. Our results show outperforms at identifying genes enriched pathways significantly associated reconstruction drives improvement capture diet-related compared when implemented without user input phenotype evolution. will provide strong foundation applying larger data sets complex trait have previously been analyzed.

Language: Английский

Convergent genomic signatures associated with vertebrate viviparity DOI Creative Commons
Rhiannon V. Eastment, Bob B. M. Wong,

Matthew D. McGee

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Feb. 8, 2024

Abstract Background Viviparity—live birth—is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree Life. Viviparous species exhibit remarkable levels reproductive diversity, both in amount care provided by parent during gestation, ways which is delivered. The genetic basis viviparity garnered increasing interest over recent years; however, such studies are often undertaken on small evolutionary timelines, thus not able to address changes occurring broader scale. Using whole genome data, we investigated molecular this innovation diversity vertebrates answer long held question biology: evolution convergent traits driven genomic changes? Results We reveal protein family sizes, protein-coding regions, introns, untranslated regions (UTRs) number distantly related viviparous lineages. Specifically, identify 15 families showing evidence contraction or expansion associated with viviparity. additionally elevated substitution rates coding noncoding sequences several However, did find any changes—be it at nucleotide level—common all Conclusions Our results highlight value macroevolutionary comparative genomics determining transitions. While may be vertebrates, there does appear signature shared vertebrates. Ultimately, our findings indicate trait as likely evolves multiple different pathways.

Language: Английский

Citations

4
Whole-genome sequencing and phenotyping reveal specific adaptations ofLachancea thermotoleransto the winemaking environment DOI Creative Commons
Javier Vicente, Anne Friedrich, Joseph Schacherer

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 1, 2024

ABSTRACT Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures. Lachancea thermotolerans , related fermentative process and one current trends wine technology research, has undergone anthropization that led strong differentiation both from genomic phenomic perspective. Using whole-genome sequencing, we have investigated diversity 145 L. strains, identifying six well-defined groups primarily delineated by their ecological origin exhibiting high levels genetic diversity. Anthropized strains showed lower due purifying selection imposed winemaking environment. Strong evidence adaptation through modification gene content was also found. Differences genes involved assimilation alternative carbon nitrogen sources, such MAL1 DAL5 genes, which confer greater fitness environment, were observed. Additionally, found phenotypic traits considered domestication hallmarks are present anthropized strains. Among these, increased presence ethanol sulphites, non-fermentable sources glycerol, residual fructose under conditions highlight. We hypothesize lactic acid production wine-related is signature adaption early Crabtree-positive yeasts Overall, results this work provide valuable insight into demonstrate how fermentation environments give rise similar adaptations different species.

Language: Английский

Citations

2
Evidence for gene flow and trait reversal during radiation of Mexican Goodeid fish DOI Creative Commons
Leeban H. Yusuf, Yolitzi Saldívar Lemus, Peter Thorpe

et al.

Heredity, Journal Year: 2024, Volume and Issue: unknown

Published: June 10, 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
Modes of Reproduction in Vertebrates: Oviparity, Viviparity, Hermaphroditism, Parthenogenesis (General Definition With Examples) DOI
Marvalee H. Wake

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Language: Английский

Citations

0
RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution DOI Creative Commons
Ruby Redlich, Amanda Kowalczyk,

Michael Tene

et al.

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(11)

Published: Oct. 15, 2024

Comparative genomics approaches seek to associate molecular evolution with the of phenotypes across a phylogeny. Many these methods lack ability analyze non-ordinal categorical traits more than two categories. To address this limitation, we introduce an expansion RERconverge that associates shifts in evolutionary rates convergent traits. The includes for performing ancestral state reconstruction, statistical tests associating relative variables, and new method phylogeny-aware permutations, "permulations", on We demonstrate our three-category diet phenotype, compare its performance binary analyses existing comparative genomic traits: phylogenetic simulations signal based method. present analysis how permulations scale number species categories included analysis. Our results show outperforms at identifying genes enriched pathways significantly associated reconstruction drives improvement capture diet-related compared when implemented without user input phenotype evolution. will provide strong foundation applying larger data sets complex trait have previously been analyzed.

Language: Английский

Citations

0