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1. A fast‐evolving X‐linked duplicate of importin‐α2 is overexpressed in sex‐ratio drive in Drosophila neotestacea

   https://doi.org/10.1111/mec.14928  

   Pieper, Kathleen E.; Unckless, Robert L.; Dyer, Kelly A. (December 2018, Molecular Ecology)

   Abstract Selfish genetic elements that manipulate gametogenesis to achieve a transmission advantage are known as meiotic drivers.Sex‐ratioX chromosomes (SR) are meiotic drivers that prevent the maturation of Y‐bearing sperm in male carriers to result in the production of mainly female progeny. The spread of an SR chromosome can affect host genetic diversity and genome evolution, and can even cause host extinction if it reaches sufficiently high prevalence. Meiotic drivers have evolved independently many times, though only in a few cases is the underlying genetic mechanism known. In this study we use a combination of transcriptomics and population genetics to identify widespread expression differences between the standard (ST) andsex‐ratio(SR) X chromosomes of the flyDrosophila neotestacea.We found the X chromosome is enriched for differentially expressed transcripts and that many of these X‐linked differentially expressed transcripts had elevatedK_a/K_svalues between ST and SR, indicative of potential functional differences. We identified a set of candidate transcripts, including a testis‐specific, X‐linked duplicate of the nuclear transport geneimportin‐α2that is overexpressed in SR.We find suggestions of positive selection in the lineage leading to the duplicate and that its molecular evolutionary patterns are consistent with relaxed purifying selection in ST. As these patterns are consistent with involvement in the mechanism of drive in this species, this duplicate is a strong candidate worthy of further functional investigation. Nuclear transport may be a common target for genetic conflict, as the mechanism of the autosomalSegregation Distorterdrive system inD. melanogasterinvolves the same pathway. 

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2. Biotic and anthropogenic forces rival climatic/abiotic factors in determining global plant population growth and fitness

   https://doi.org/10.1073/pnas.1918363117  

   Morris, William F.; Ehrlén, Johan; Dahlgren, Johan P.; Loomis, Alexander K.; Louthan, Allison M. (January 2020, Proceedings of the National Academy of Sciences)

   Multiple, simultaneous environmental changes, in climatic/abiotic factors, interacting species, and direct human influences, are impacting natural populations and thus biodiversity, ecosystem services, and evolutionary trajectories. Determining whether the magnitudes of the population impacts of abiotic, biotic, and anthropogenic drivers differ, accounting for their direct effects and effects mediated through other drivers, would allow us to better predict population fates and design mitigation strategies. We compiled 644 paired values of the population growth rate ( λ ) from high and low levels of an identified driver from demographic studies of terrestrial plants. Among abiotic drivers, natural disturbance (not climate), and among biotic drivers, interactions with neighboring plants had the strongest effects on λ . However, when drivers were combined into the 3 main types, their average effects on λ did not differ. For the subset of studies that measured both the average and variability of the driver, λ was marginally more sensitive to 1 SD of change in abiotic drivers relative to biotic drivers, but sensitivity to biotic drivers was still substantial. Similar impact magnitudes for abiotic/biotic/anthropogenic drivers hold for plants of different growth forms, for different latitudinal zones, and for biomes characterized by harsher or milder abiotic conditions, suggesting that all 3 drivers have equivalent impacts across a variety of contexts. Thus, the best available information about the integrated effects of drivers on all demographic rates provides no justification for ignoring drivers of any of these 3 types when projecting ecological and evolutionary responses of populations and of biodiversity to environmental changes. 

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3. Supergene potential of a selfish centromere

   https://doi.org/10.1098/rstb.2021.0208  

   Finseth, Findley; Brown, Keely; Demaree, Andrew; Fishman, Lila (August 2022, Philosophical Transactions of the Royal Society B: Biological Sciences)

   Selfishly evolving centromeres bias their transmission by exploiting the asymmetry of female meiosis and preferentially segregating to the egg. Such female meiotic drive systems have the potential to be supergenes, with multiple linked loci contributing to drive costs or enhancement. Here, we explore the supergene potential of a selfish centromere ( D ) in Mimulus guttatus , which was discovered in the Iron Mountain (IM) Oregon population. In the nearby Cone Peak population, D is still a large, non-recombining and costly haplotype that recently swept, but shorter haplotypes and mutational variation suggest a distinct population history. We detected D in five additional populations spanning more than 200 km; together, these findings suggest that selfish centromere dynamics are widespread in M. guttatus . Transcriptome comparisons reveal elevated differences in expression between driving and non-driving haplotypes within, but not outside, the drive region, suggesting large-scale cis effects of D 's spread on gene expression. We use the expression data to refine linked candidates that may interact with drive, including Nuclear Autoantigenic Sperm Protein (NASP SIM3 ), which chaperones the centromere-defining histone CenH3 known to modify Mimulus drive. Together, our results show that selfishly evolving centromeres may exhibit supergene behaviour and lay the foundation for future genetic dissection of drive and its costs. This article is part of the theme issue ‘Genomic architecture of supergenes: causes and evolutionary consequences’. 

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4. 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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5. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias )

   https://doi.org/10.1093/sysbio/syaa085  

   Sarver, Brice A; Herrera, Nathanael D; Sneddon, David; Hunter, Samuel S; Settles, Matthew L; Kronenberg, Zev; Demboski, John R; Good, Jeffrey M; Sullivan, Jack (January 2021, Systematic Biology)

   Kubatko, Laura (Ed.)

   Abstract Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (Tamias canipes, Tamias cinereicollis, Tamias dorsalis, T. quadrivittatus, Tamias rufus, and Tamias umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population-genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group. [Cytonuclear discordance; hyridization; introgression, phylogenomics; SVDquartets; Tamias.] 

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