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1. pSONIC: Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity

   https://doi.org/10.1093/g3journal/jkab170  

   Conover, Justin L; Sharbrough, Joel; Wendel, Jonathan F (May 2021, G3 Genes|Genomes|Genetics)

   Morrell, P L (Ed.)

   Abstract With the rapid rise in availability of high-quality genomes for closely related species, methods for orthology inference that incorporate synteny are increasingly useful. Polyploidy perturbs the 1:1 expected frequencies of orthologs between two species, complicating the identification of orthologs. Here we present a method of ortholog inference, Ploidy-aware Syntenic Orthologous Networks Identified via Collinearity (pSONIC). We demonstrate the utility of pSONIC using four species in the cotton tribe (Gossypieae), including one allopolyploid, and place between 75% and 90% of genes from each species into nearly 32,000 orthologous groups, 97% of which consist of at most singletons or tandemly duplicated genes—58.8% more than comparable methods that do not incorporate synteny. We show that 99% of singleton gene groups follow the expected tree topology and that our ploidy-aware algorithm recovers 97.5% identical groups when compared to splitting the allopolyploid into its two respective subgenomes, treating each as separate “species.” 

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2. Shared single copy genes are generally reliable for inferring phylogenetic relationships among polyploid taxa

   https://doi.org/10.1016/j.ympev.2024.108087  

   Naranjo, Jaells G; Sither, Charles B; Conant, Gavin C (July 2024, Molecular Phylogenetics and Evolution)

   Polyploidy, or whole-genome duplication, is expected to confound the inference of species trees with phyloge- netic methods for two reasons. First, the presence of retained duplicated genes requires the reconciliation of the inferred gene trees to a proposed species tree. Second, even if the analyses are restricted to shared single copy genes, the occurrence of reciprocal gene loss, where the surviving genes in different species are paralogs from the polyploidy rather than orthologs, will mean that such genes will not have evolved under the corresponding species tree and may not produce gene trees that allow inference of that species tree. Here we analyze three different ancient polyploidy events, using synteny-based inferences of orthology and paralogy to infer gene trees from nearly 17,000 sets of homologous genes. We find that the simple use of single copy genes from polyploid organisms provides reasonably robust phylogenetic signals, despite the presence of reciprocal gene losses. Such gene trees are also most often in accord with the inferred species relationships inferred from maximum likelihood models of gene loss after polyploidy: a completely distinct phylogenetic signal present in these genomes. As seen in other studies, however, we find that methods for inferring phylogenetic confidence yield high support values even in cases where the underlying data suggest meaningful conflict in the phylogenetic signals. 

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3. Convergent evolution of polyploid genomes from across the eukaryotic tree of life

   https://doi.org/10.1093/g3journal/jkac094  

   Hao, Yue; Fleming, Jonathon; Petterson, Joanna; Lyons, Eric; Edger, Patrick_P; Pires, J_Chris; Thorne, Jeffrey_L; Conant, Gavin_C; Morrell, ed., P. (April 2022, G3 Genes|Genomes|Genetics)

   Abstract By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts. We show that many of the events show a relative rate of duplicate gene loss before the first postpolyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate postpolyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with 2 distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is, therefore, possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass reciprocal gene loss barriers. 

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4. A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes

   https://doi.org/10.1186/s12859-022-04635-9  

   Clark, Lindsay V.; Mays, Wittney; Lipka, Alexander E.; Sacks, Erik J. (March 2022, BMC Bioinformatics)

   Abstract BackgroundGiven the economic and environmental importance of allopolyploids and other species with highly duplicated genomes, there is a need for methods to distinguish paralogs, i.e. duplicate sequences within a genome, from Mendelian loci, i.e. single copy sequences that pair at meiosis. The ratio of observed to expected heterozygosity is an effective tool for filtering loci but requires genotyping to be performed first at a high computational cost, whereas counting the number of sequence tags detected per genotype is computationally quick but very ineffective in inbred or polyploid populations. Therefore, new methods are needed for filtering paralogs. ResultsWe introduce a novel statistic,H_ind/H_E, that uses the probability that two reads sampled from a genotype will belong to different alleles, instead of observed heterozygosity. The expected value ofH_ind/H_Eis the same across all loci in a dataset, regardless of read depth or allele frequency. In contrast to methods based on observed heterozygosity, it can be estimated and used for filtering loci prior to genotype calling. In addition to filtering paralogs, it can be used to filter loci with null alleles or high overdispersion, and identify individuals with unexpected ploidy and hybrid status. We demonstrate that the statistic is useful at read depths as low as five to 10, well below the depth needed for accurate genotype calling in polyploid and outcrossing species. ConclusionsOur methodology for estimatingH_ind/H_Eacross loci and individuals, as well as determining reasonable thresholds for filtering loci, is implemented in polyRAD v1.6, available athttps://github.com/lvclark/polyRAD. In large sequencing datasets, we anticipate that the ability to filter markers and identify problematic individuals prior to genotype calling will save researchers considerable computational time. 

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5. Porosity Evolution in Rate and State Friction

   https://doi.org/10.1029/2022GL101056  

   Rudnicki, John W. (November 2022, Geophysical Research Letters)

   Abstract This letter compares the predictions of two expressions proposed for the porosity evolution in the context of rate and state friction. One (Segall & Rice, 1995,https://doi.org/10.1029/95jb02403) depends only on the sliding velocity; the other (Sleep, 1995,https://doi.org/10.1029/94jb03340) depends only on the state variable. Simulations of both are similar for velocity stepping and slide‐hold‐slide experiments. They differ significantly for normal effective stress jumps at constant sliding velocity. Segall and Rice (1995,https://doi.org/10.1029/95jb02403) predicts no change in the porosity; Sleep (1995,https://doi.org/10.1029/94jb03340) does. Simulation with a spring‐block model indicates that the magnitude of rapid slip events is essentially the same for the two formulations. Variations of porosity and induced pore pressure near rapid slip events are similar and consistent with experimental observations. Predicted porosity variations during slow slip intervals and the time at which rapid slip events occur are significantly different. The simulation indicates that changes in friction stress due to pore pressure changes exceed those due to rate and state effects. 

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