HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Pond, Sergei L. Kosakovsky; Poon, Art F. Y.; Velazquez, Ryan; Weaver, Steven; Hepler, N. Lance; Murrell, Ben; Shank, Stephen D; Magalis, Brittany Rife; Bouvier, Dave; Nekrutenko, Anton; Wisotsky, Sadie; Spielman, Scott R.; Frost, Sally; Muse, Spencer V.

doi:10.1093/molbev/msz197

Cited by 416 publications

(336 citation statements)

References 23 publications

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“…Thus, attaining additional population data and whole genomes of multiple Tribolium species will be valuable for allowing further tests of putative positive selection on the X chromosome using complementary approaches to the ones employed here. These methods could include, for example, McDonald-Kreitman tests (Mcdonald and Kreitman 1991;Meisel and Connallon 2013;Rousselle et al 2016;Murga-Moreno et al 2019;Pinharanda et al 2019) and branch-site analyses of dN/dS in multiple species (Yang 2007;Kosakovsky Pond et al 2019). Population data analyses will also allow measures of recombination rates (Stumpf and Mcvean 2003;Comeron et al 2012), which has been suggested to influence the faster-X effect ) and assessments of potential roles of effective population size (Mank et al 2010b).…”

Section: Discussionmentioning

confidence: 99%

Absence of a Faster-X Effect in Beetles (Tribolium, Coleoptera)

Whittle

Kulkarni

Extavour

2020

G3 Genes|Genomes|Genetics

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The faster-X effect, namely the rapid evolution of protein-coding genes on the X chromosome, has been widely reported in metazoans. However, the prevalence of this phenomenon across diverse systems and its potential causes remain largely unresolved. Analysis of sex-biased genes may elucidate its possible mechanisms: for example, in systems with X/Y males a more pronounced faster-X effect in male-biased genes than in female-biased or unbiased genes may suggest fixation of recessive beneficial mutations rather than genetic drift. Further, theory predicts that the faster-X effect should be promoted by X chromosome dosage compensation. Here, we asked whether we could detect a faster-X effect in genes of the beetle Tribolium castaneum (and T. freemani orthologs), which has X/Y sex-determination and heterogametic males. Our comparison of protein sequence divergence (dN/dS) on the X chromosome vs. autosomes indicated a rarely observed absence of a faster-X effect in this organism. Further, analyses of sex-biased gene expression revealed that the X chromosome was particularly highly enriched for ovary-biased genes, which evolved slowly. In addition, an evaluation of male X chromosome dosage compensation in the gonads and in non-gonadal somatic tissues indicated a striking lack of compensation in the testis. This under-expression in testis may limit fixation of recessive beneficial X-linked mutations in genes transcribed in these male sex organs. Taken together, these beetles provide an example of the absence of a faster-X effect on protein evolution in a metazoan, that may result from two plausible factors, strong constraint on abundant X-linked ovary-biased genes and a lack of gonadal dosage compensation.

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Section: Discussionmentioning

confidence: 99%

Absence of a Faster-X Effect in Beetles (Tribolium, Coleoptera)

Whittle

Kulkarni

Extavour

2020

G3 Genes|Genomes|Genetics

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“…Additionally, to determine whether bats, and specifically the family Rhinolophidae, are under strong selection to adapt to viruses we used the adaptive branch-site random effects model test of positive selection, aBSREL 21 , as implemented in HyPhy, version 2.5.8 41 , using a pruned subset of five phylogenetic hypotheses chosen from the pseudo-posterior distribution of Upham et al 17 to account for phylogenetic uncertainty. We tested three conditions: 1) in which the branch leading to Rhinolophidae was considered the foreground branch; 2) in which the branch leading to the common ancestor of all bats was considered the foreground branch; and 3) in which all branches were tested without a priori specification of background and foreground branches.…”

Section: Experimental Methodsmentioning

confidence: 99%

Exceptional diversity and selection pressure on SARS-CoV and SARS-CoV-2 host receptor in bats compared to other mammals

Frank

Enard

2020

Preprint

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9Pandemics originating from pathogen transmission between animals and humans 10 highlight the broader need to understand how natural hosts have evolved in response to 11 emerging human pathogens and which groups may be susceptible to infection. Here, we 12 investigate angiotensin-converting enzyme 2 (ACE2), the host protein bound by SARS-CoV and 13 SARS-CoV-2. We find that the ACE2 gene is under strong selection pressure in bats, the group 14 in which the progenitors of SARS-CoV and SARS-CoV-2 are hypothesized to have evolved, 15 particularly in residues that contact SARS-CoV and SARS-CoV-2. We detect positive selection 16 in non-bat mammals in ACE2 but in a smaller proportion of branches than in bats, without 17 enrichment of selection in residues that contact SARS-CoV or SARS-CoV-2. Additionally, we 18 evaluate similarity between humans and other species in residues that contact SARS-CoV or 19 SARS-CoV-2, revealing potential susceptible species but also highlighting the difficulties of 20 predicting spillover events. This work increases our understanding of the relationship between 21 mammals, particularly bats, and coronaviruses, and provides data that can be used in functional 22 studies of how host proteins are bound by SARS-CoV and SARS-CoV-2 strains.23 24 Main: 25 The recent coronavirus pandemic has highlighted the disastrous impacts of zoonotic 26 spillovers and underscores the need to understand how pathogens and hosts evolve in 27 response to one another. Evolutionary analyses of host proteins targeted by infections reveal 28 the pressures that hosts have faced from pathogens and how they have evolved to resist 29 disease, informing predictions about spread of infections and how to counter them. The virus, 30SARS-CoV-2, the causative virus of COVID-19, like its close relative SARS-CoV, is thought to 31 have its progenitor origins in bats 1-3 . Bats have been suggested to be "special" reservoirs of 32 emerging infectious viruses 4 and of coronaviruses in particular 5 . However, often this species-33 rich, ecologically diverse clade is treated as a homogenous group, represented by one or two 34 was not certified by peer review) : bioRxiv preprint species, particularly when considering the interaction of SARS-CoV and SARS-CoV-2 with host 35 proteins (but see Hou et al. 6 and Demogines et al. 7 which consider multiple bat species). 36Examination of host proteins bound by potential zoonoses can be used not only to infer 37 past and current evolutionary pressure but to inform the likelihood of cross-species 38 transmission. One major barrier to cross-species transmission is the ability of the virus, adapted 39 to one host protein, to bind another species' protein 8,9 . Accordingly, many studies have 40 examined the ACE2 sequence of suspected disease reservoirs to understand how different viral 41 strains bind different species' ACE2 and where zoonotic spillover may have originated 6,8,10-12 . 42These studies, especially ones involving functional assays or in-depth modeling of virus-host 43 contacts, are usual...

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“…1.6.10; with option -bb 10000 -alrt 1000). The evidence for selection across gene families was tested using the HyPhy 112,113 platform in the webserver of datamonkey 114–116 . According to the recombination breakpoints analysed by the Genetic Algorithm for Recombination Detection 117 (GARD), the alignment was trimmed for analysing selection using Single-Likelihood Ancestor Counting 118 (SLAC) and Mixed Effects Model of Evolution 119 (MEME) with P <0.1.…”

Section: Methodsmentioning

confidence: 99%

Mycena genomes resolve the evolution of fungal bioluminescence

Lee

Lin

et al. 2020

Preprint

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24Mushroom-forming fungi in the order Agaricales represent an independent origin of 25 bioluminescence in the tree of life, yet the diversity, evolutionary history, and timing of 26 the origin of fungal luciferases remain elusive. We sequenced the genomes and 27transcriptomes of five bonnet mushroom species (Mycena spp.), a diverse lineage 28comprising the majority of bioluminescent fungi. We show that bioluminescence 29 evolved in the common ancestor of Mycena spp. and the marasmioid clade of 30Agaricales and was maintained through at least 160 million years of evolution. We 31revealed Mycena exhibit two-speed genomes and resolve how the luciferase cluster was 32 derived by duplication and translocation, frequently rearranged and lost in most Mycena 33 species, but conserved in the Armillaria lineage. Luciferase cluster members were co-34 expressed across developmental stages, with highest expression in fruiting body caps 35and stipes, suggesting fruiting-related adaptive functions. Our results contribute to 36 understanding a de novo origin of bioluminescence and the corresponding gene cluster 37 in a diverse group of enigmatic fungal species. 38

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HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Cited by 416 publications

References 23 publications

Absence of a Faster-X Effect in Beetles (Tribolium, Coleoptera)

Absence of a Faster-X Effect in Beetles (Tribolium, Coleoptera)

Exceptional diversity and selection pressure on SARS-CoV and SARS-CoV-2 host receptor in bats compared to other mammals

Mycena genomes resolve the evolution of fungal bioluminescence

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