scholarly journals phydms: Software for phylogenetic analyses informed by deep mutational scanning

2017 ◽  
Author(s):  
Sarah K. Hilton ◽  
Michael B Doud ◽  
Jesse D Bloom
Keyword(s):  
Gene Evolution ◽  
Phylogenetic Analyses ◽  
Quantitative Comparison ◽  
Experimental Measurements ◽  
Protein Coding ◽  
Site Specific ◽  
Protein Coding Genes ◽  
Phylogenetic Methods ◽  
Substitution Models ◽  
Actual Selection

AbstractBackgroundThe evolution of protein-coding genes can be quantitatively modeled using phylogenetic methods. Recently, it has been shown that high-throughput experimental measurements of mutational effects made via deep mutational scanning can inform site-specific phylogenetic substitution models of gene evolution. However, there is currently no software tailored for such analyses.ResultsWe describe software that efficiently performs phylogenetic analyses with substitution models informed by deep mutational scanning. This software, phydms, is ∼100-fold faster than existing programs that accommodate such substitution models. It can be used to compare the results of deep mutational scanning experiments to the selection on genes in nature. For instance, phydms enables rigorous comparison of how well different experiments on the same gene describe natural selection. It also enables the re-scaling of deep mutational scanning data to account for differences in the stringency of selection in the lab and nature. Finally, phydms can identify sites that are evolving differently in nature than expected from experiments in the lab.ConclusionsThe phydms software makes it easy to use phylogenetic substitution models informed by deep mutational scanning experiments. As data from such experiments becomes increasingly widespread, phydms will facilitate quantitative comparison of the experimental results to the actual selection pressures shaping evolution in nature.

scholarly journals phydms: software for phylogenetic analyses informed by deep mutational scanning

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3657 ◽  
Author(s):  
Sarah K. Hilton ◽  
Michael B. Doud ◽  
Jesse D. Bloom
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Gene Evolution ◽  
Phylogenetic Analyses ◽  
Point Mutations ◽  
Quantitative Comparison ◽  
Experimental Measurements ◽  
Site Specific ◽  
Substitution Models ◽  
Actual Selection

It has recently become possible to experimentally measure the effects of all amino-acid point mutations to proteins using deep mutational scanning. These experimental measurements can inform site-specific phylogenetic substitution models of gene evolution in nature. Here we describe software that efficiently performs analyses with such substitution models. This software, phydms, can be used to compare the results of deep mutational scanning experiments to the selection on genes in nature. Given a phylogenetic tree topology inferred with another program, phydms enables rigorous comparison of how well different experiments on the same gene capture actual natural selection. It also enables re-scaling of deep mutational scanning data to account for differences in the stringency of selection in the lab and nature. Finally, phydms can identify sites that are evolving differently in nature than expected from experiments in the lab. As data from deep mutational scanning experiments become increasingly widespread, phydms will facilitate quantitative comparison of the experimental results to the actual selection pressures shaping evolution in nature.

Mitogenome of Alaudala cheleensis (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes

Zootaxa ◽  
2021 ◽  
Vol 4952 (2) ◽  
pp. 331-353
Author(s):  
CHAO YANG ◽  
LE ZHAO ◽  
QINGXIONG WANG ◽  
HAO YUAN ◽  
XUEJUAN LI ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Gene Order ◽  
Phylogenetic Relationships ◽  
Gene Rearrangement ◽  
Phylogenetic Analyses ◽  
Protein Coding ◽  
Comparative Analyses ◽  
Protein Coding Genes ◽  
Basal Position

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. There was slightly higher A+T content than that of G+C in the mitogenome, with an obvious C skew. The ATG codon initiated all protein-coding genes, while six terminating codons were used. The secondary structure of rrnS contained three domains and 47 helices, whereas rrnL included six domains and 60 helices. All tRNAs could be folded into a classic clover-leaf secondary structure except for trnS (AGY). The CR1 could be divided into three domains, including several conserved boxes (C-string, F, E, D, C and B-box, Bird similarity box, CSB1). Comparative analyses within Sylvioidea mitogenomes showed that most mitochondrial features were consistent with that of the A. cheleensis mitogenome. The basal position of the Alaudidae within the Sylvioidea in our phylogenetic analyses is consistent with other recent studies. 

scholarly journals Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10364
Author(s):  
Natalia I. Abramson ◽  
Fedor N. Golenishchev ◽  
Semen Yu. Bodrov ◽  
Olga V. Bondareva ◽  
Evgeny A. Genelt-Yanovskiy ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Morphological Characters ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Skull Morphology ◽  
Protein Coding ◽  
Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

scholarly journals A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

2020 ◽  
Author(s):  
Nicolas Rodrigue ◽  
Thibault Latrille ◽  
Nicolas Lartillot
Keyword(s):  
Adaptive Evolution ◽  
Real Data ◽  
Data Sets ◽  
Protein Coding ◽  
Site Specific ◽  
Protein Coding Genes ◽  
Codon Substitution ◽  
Selection Framework ◽  
Dna Alignment ◽  
The Impact

Abstract In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.

Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae)

2010 ◽  
Vol 61 (9) ◽  
pp. 980 ◽  
Author(s):  
Catherine J. Nock ◽  
Martin S. Elphinstone ◽  
Stuart J. Rowland ◽  
Peter R. Baverstock
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxonomic Revision ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Allopatric Populations ◽  
Murray Darling Basin ◽  
Murray Cod ◽  
Australian Freshwater

Determining the phylogenetic and taxonomic relationships among allopatric populations can be difficult, especially when divergence is recent and morphology is conserved. We used mitochondrial sequence data from the control region and three protein-coding genes (1253 bp in total) and genotypes determined at 13 microsatellite loci to examine the evolutionary relationships among Australia’s largest freshwater fish, the Murray cod, Maccullochella peelii peelii, from the inland Murray–Darling Basin, and its allopatric sister taxa from coastal drainages, the eastern freshwater cod, M. ikei, and Mary River cod, M. peelii mariensis. Phylogenetic analyses provided strong support for taxon-specific clades, with a clade containing both of the eastern taxa reciprocally monophyletic to M. peelii peelii, suggesting a more recent common ancestry between M. ikei and M. peelii mariensis than between the M. peelii subspecies. This finding conflicts with the existing taxonomy and suggests that ancestral Maccullochella crossed the Great Dividing Range in the Pleistocene and subsequently diverged in eastern coastal drainages. Evidence from the present study, in combination with previous morphological and allozymatic data, demonstrates that all extant taxa are genetically and morphologically distinct. The taxonomy of Maccullochella is revised, with Mary River cod now recognised as a species, Maccullochella mariensis, a sister species to eastern freshwater cod, M. ikei. As a result of the taxonomic revision, Murray cod is M. peelii.

scholarly journals Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

2018 ◽  
Vol 19 (8) ◽  
pp. 2383 ◽  
Author(s):  
Qixiang Lu ◽  
Wenqing Ye ◽  
Ruisen Lu ◽  
Wuqin Xu ◽  
Yingxiong Qiu
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Early Pleistocene ◽  
Disjunct Distribution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Protein Coding Genes

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

Do genomic datasets resolve the correct relationship among the placental, marsupial and monotreme lineages?

2009 ◽  
Vol 57 (4) ◽  
pp. 167 ◽  
Author(s):  
Gavin Huttley
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Protein Coding ◽  
Substitution Models ◽  
True Tree ◽  
Molecular Phylogenetic ◽  
Tree Topologies ◽  
Mammal Evolution ◽  
Genome Projects

Did the mammal radiation arise through initial divergence of prototherians from a common ancestor of metatherians and eutherians, the Theria hypothesis, or of eutherians from a common ancestor of metatherians and prototherians, the Marsupionta hypothesis? Molecular phylogenetic analyses of point substitutions applied to this problem have been contradictory – mtDNA-encoded sequences supported Marsupionta, nuclear-encoded sequences and RY (purine–pyrimidine)-recoded mtDNA supported Theria. The consistency property of maximum likelihood guarantees convergence on the true tree only with longer alignments. Results from analyses of genome datasets should therefore be impervious to choice of outgroup. We assessed whether important hypotheses concerning mammal evolution, including Theria/Marsupionta and the branching order of rodents, carnivorans and primates, are resolved by phylogenetic analyses using ~2.3 megabases of protein-coding sequence from genome projects. In each case, only two tree topologies were being compared and thus inconsistency in resolved topologies can only derive from flawed models of sequence divergence. The results from all substitution models strongly supported Theria. For the eutherian lineages, all models were sensitive to the outgroup. We argue that phylogenetic inference from point substitutions will remain unreliable until substitution models that better match biological mechanisms of sequence divergence have been developed.

scholarly journals Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Genes ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 115
Author(s):  
Yuxin Hu ◽  
Weiyue Xing ◽  
Zhengyu Hu ◽  
Guoxiang Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Phylogenetic Relationship ◽  
Phylogenetic Analyses ◽  
Mitochondrial Protein ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Genomes ◽  
Volvocine Algae

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

scholarly journals Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change

2020 ◽  
Vol 66 (5) ◽  
pp. 505-514
Author(s):  
Laurel R Yohe ◽  
Matteo Fabbri ◽  
Michael Hanson ◽  
Bhart-Anjan S Bhullar
Keyword(s):  
Olfactory Receptor ◽  
Chemical Cues ◽  
Gene Evolution ◽  
Chemical Space ◽  
Morphological Data ◽  
Phenotypic Change ◽  
Phenotypic Traits ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Or Genes

Abstract Chemosensation is the most ubiquitous sense in animals, enacted by the products of complex gene families that detect environmental chemical cues and larger-scale sensory structures that process these cues. While there is a general conception that olfactory receptor (OR) genes evolve rapidly, the universality of this phenomenon across vertebrates, and its magnitude, are unclear. The supposed correlation between molecular rates of chemosensory evolution and phenotypic diversity of chemosensory systems is largely untested. We combine comparative genomics and sensory morphology to test whether OR genes and olfactory phenotypic traits evolve at faster rates than other genes or traits. Using published genomes, we identified ORs in 21 tetrapods, including amphibians, reptiles, birds, and mammals and compared their rates of evolution to those of orthologous non-OR protein-coding genes. We found that, for all clades investigated, most OR genes evolve nearly an order of magnitude faster than other protein-coding genes, with many OR genes showing signatures of diversifying selection across nearly all taxa in this study. This rapid rate of evolution suggests that chemoreceptor genes are in “evolutionary overdrive,” perhaps evolving in response to the ever-changing chemical space of the environment. To obtain complementary morphological data, we stained whole fixed specimens with iodine, µCT-scanned the specimens, and digitally segmented chemosensory and nonchemosensory brain regions. We then estimated phenotypic variation within traits and among tetrapods. While we found considerable variation in chemosensory structures, they were no more diverse than nonchemosensory regions. We suggest chemoreceptor genes evolve quickly in reflection of an ever-changing chemical space, whereas chemosensory phenotypes and processing regions are more conserved because they use a standardized or constrained architecture to receive and process a range of chemical cues.

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