TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees

Woolley, Steve; Johnson, Justin; Smith, Matthew J.; Crandall, Keith A.; McClellan, David A.

doi:10.1093/bioinformatics/btg043

Cited by 280 publications

(269 citation statements)

References 12 publications

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“…Given the strong levels of mitochondrial divergence (~12%) observed between the two inland species (Murray cod and trout cod), conservation of the same amino acid in Murray cod and trout cod for differences that were fixed across the GDR could reflect strong selective pressures for these amino acids in environments west of the GDR that are relaxed or different east of the GDR. Seven of the 13 amino acid differences fixed between the inland and coastal species were associated with significant changes in physicochemical properties (six of these changes relating to properties with evidence of positive selection based on global Z scores) suggesting that functional differences exist between mitogenomes east and west of the GDR that may have consequences for metabolic function (Woolley et al, 2003).…”

Section: Discussionmentioning

confidence: 99%

“…Because ω ratios 41 may not reflect molecular adaptation per se, we used TREESAAP (Woolley et al, 2003) to look for significant changes in physicochemical properties associated with amino acid replacements in inferred proteins on particular branches in the phylogeny. TREESAAP uses a sliding window approach to compare observed patterns of amino acid replacements and changes in physiochemical properties to those expected under neutrality (Woolley et al, 2003). Amino acid replacements that have strong effects on protein biochemistry are considered candidates for selection (Woolley et al, 2003).…”

Section: Divergence Time Estimatesmentioning

confidence: 99%

“…TREESAAP uses a sliding window approach to compare observed patterns of amino acid replacements and changes in physiochemical properties to those expected under neutrality (Woolley et al, 2003). Amino acid replacements that have strong effects on protein biochemistry are considered candidates for selection (Woolley et al, 2003). We ran the analysis with a sliding window size of 20 codons, increasing in 1-codon increments.…”

Section: Divergence Time Estimatesmentioning

confidence: 99%

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Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

et al. 2016

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Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in geneticsbased metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid-to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.

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Section: Discussionmentioning

confidence: 99%

Section: Divergence Time Estimatesmentioning

confidence: 99%

Section: Divergence Time Estimatesmentioning

confidence: 99%

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Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

et al. 2016

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“…We used the program TreeSAAP v3.2 (McClellan and Ellison, 2010;Woolley et al, 2003) to test for selection within the aligned opsin datasets used for phylogeny reconstruction on the 12 specific amino acid properties controlling protein compressibility (see above for list).…”

Section: Identifying Selective Influences Due To Hydrostatic Pressurementioning

confidence: 99%

“…To investigate if this relationship is due to an intrinsic adaptation in protein structure, we used further comparative evolutionary statistical methods (Woolley et al, 2003) to look for evidence of positive destabilizing selection acting on the twelve amino acid properties that define overall protein compressibility (Gromiha and Ponnuswamy, 1993). Positive destabilizing selection is defined as selection for radical change in specific amino acid properties (e.g.…”

Section: Positive Selection On the Physiochemical Properties That Defmentioning

confidence: 99%

Evolution under pressure and the adaptation of visual pigment compressibility in deep-sea environments

Porter

Roberts

Partridge

2016

Molecular Phylogenetics and Evolution

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Understanding the link between how proteins function in animals that live in extreme environments and selection on specific properties of amino acids has proved extremely challenging. Here we present the discovery of how the compressibility of opsin proteins in two evolutionarily distinct animal groups, teleosts and cephalopods, appears to be adapted to the high-pressure environment of the deep-sea. We report how in both groups, opsins in deeper living species are calculated to be less compressible. This is largely due to a common set of amino acid sites (bovRH#159, 196, 213, 275) undergoing positive destabilizing selection in six of the twelve amino acid physiochemical properties that determine protein compressibility. This suggests a common evolutionary mechanism to reduce the adiabatic compressibility of opsin proteins. Intriguingly, the sites under selection are on the proteins' outer faces at locations known to be involved in opsin-opsin dimer interactions.

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Cloning, characterization, and evolutionary patterns of KCNQ4 genes in anurans

Guo,

Zhu,

Shen

et al. 2024

Ecology and Evolution

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Acoustic communication plays important roles in the survival and reproduction of anurans. The perception and discrimination of conspecific sound signals of anurans were always affected by masking background noise. Previous studies suggested that some frogs evolved the high‐frequency hearing to minimize the low‐frequency noise. However, the molecular mechanisms underlying the high‐frequency hearing in anurans have not been well explored. Here, we cloned and obtained the coding regions of a high‐frequency hearing‐related gene (KCNQ4) from 11 representative anuran species and compared them with orthologous sequences from other four anurans. The sequence characteristics and evolutionary analyses suggested the highly conservation of the KCNQ4 gene in anurans, which supported their functional importance. Branch‐specific analysis showed that KCNQ4 genes were under different evolutionary forces in anurans and most anuran lineages showed a generally strong purifying selection. Intriguingly, one significantly positively selected site was identified in the anuran KCNQ4 gene based on FEL model. Positive selection was also found along the common ancestor of Ranidae and Rhacophoridae as well as the ancestral O. tianmuii based on the branch‐site analysis, and the positively selected sites identified were involved in or near the N‐terminal ion transport and the potassium ion channel functional domain of the KCNQ4 genes. The present study revealed valuable information regarding the KCNQ4 genes in anurans and provided some new insights for the underpinnings of the high‐frequency hearing in frogs.

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TreeSAAP: Selection on Amino Acid Properties using phylogenetic trees

Abstract: The software program TreeSAAP measures the selective influences on 31 structural and biochemical amino acid properties during cladogenesis, and performs goodness-of-fit and categorical statistical tests.

Cited by 280 publications

References 12 publications

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

Evolution under pressure and the adaptation of visual pigment compressibility in deep-sea environments

Cloning, characterization, and evolutionary patterns of KCNQ4 genes in anurans

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