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Link Your Sites (LYS) Scripts: Automated Search of Protein Structures and Map** of Sites Under Positive Selection Detected by PAML
The visualization of the molecular context of an amino acid mutation in a protein structure is crucial for the assessment of its functional impact...
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Molecular Evolutionary Study: Phylogenetic Tree
This chapter discusses mostly the molecular evolutionary studies with biodiversity analysis through phylogenetic tree construction. The commonly used...
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Investigating the reliability of molecular estimates of evolutionary time when substitution rates and speciation rates vary
BackgroundAn accurate timescale of evolutionary history is essential to testing hypotheses about the influence of historical events and processes,...
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PoSE: visualization of patterns of sequence evolution using PAML and MATLAB
BackgroundDetermining patterns of nucleotide and amino acid substitution is the first step during sequence evolution analysis. However, it is not...
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Convergent genomic signatures associated with vertebrate viviparity
BackgroundViviparity—live birth—is a complex and innovative mode of reproduction that has evolved repeatedly across the vertebrate Tree of Life....
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Functional Divergence and Origin of the Vertebrate Praja Family
The Praja family is an E3 ubiquitin ligase, promoting polyubiquitination and subsequent degradation of substrates. It comprises two paralogs, praja1...
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Evolutionary analysis of the mTOR pathway provide insights into lifespan extension across mammals
BackgroundLifespan extension has independently evolved several times during mammalian evolution, leading to the emergence of a group of long-lived...
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A chromosome-level genome of electric catfish (Malapterurus electricus) provided new insights into order Siluriformes evolution
The electric catfish ( Malapterurus electricus ), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of...
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Genome assembly of Melilotus officinalis provides a new reference genome for functional genomics
BackgroundSweet yellow clover ( Melilotus officinalis ) is a diploid plant (2n = 16) that is native to Europe. It is an excellent legume forage. It...
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Molecular adaptations underlying high-frequency hearing in the brain of CF bats species
BackgroundThe majority of bat species have developed remarkable echolocation ability, especially for the laryngeally echolocating bats along with...
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Adaptive Selection in the Evolution of Aquaglyceroporins in Mammals
Aquaporins (AQPs) are integral membrane proteins responsible for water transport across cellular membranes in both prokaryotes and eukaryotes. A...
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Multiple Ecological Axes Drive Molecular Evolution of Cone Opsins in Beloniform Fishes
Ecological and evolutionary transitions offer an excellent opportunity to examine the molecular basis of adaptation. Fishes of the order Beloniformes...
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Positive selection-driven fixation of a hominin-specific amino acid mutation related to dephosphorylation in IRF9
The arms race between humans and pathogens drives the evolution of the human genome. It is thus expected that genes from the interferon-regulatory...
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Dating Microbial Evolution with MCMCtree
This protocol explains how to use the program MCMCtree to estimate divergence times in microbial phylogenies. The main advantage of MCMCtree is the...
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An Integrated Method to Reconstruct Ancient Proteins
Proteins have played a fundamental role throughout life’s history on Earth. Despite their biological importance, ancient origin, early function, and...
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Ancestral Sequence Reconstruction for Exploring Alkaloid Evolution
The complex and bioactive monoterpene indole alkaloids (MIAs) found in Catharanthus roseus and related species are the products of many millions of...
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A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards
Due to their integral roles in oxidative phosphorylation, mitochondrially encoded proteins represent common targets of selection in response to...
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High-quality chromosome-level de novo assembly of the Trifolium repens
BackgroundWhite clover ( Trifolium repens L. ), an excellent perennial legume forage, is an allotetraploid native to southeastern Europe and southern...
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Evolutionary genetics of pulmonary anatomical adaptations in deep-diving cetaceans
BackgroundCetaceans, having experienced prolonged adaptation to aquatic environments, have undergone evolutionary changes in their respiratory...
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The genetic basis of the leafy seadragon’s unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling
The leafy seadragon certainly is among evolution’s most “beautiful and wonderful” species aptly named for its extraordinary camouflage mimicking its...