Gradual evolution of allopolyploidy in Arabidopsis suecica.

Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution

The kinetics of L10 superstructure formation in the Cu–56Au alloy (at. %): resistometric study

Due to the improved strength properties compared to the equiatomic Cu–50 at. % Au alloy, non-stoichiometric Cu–56 at. % Au alloy can be used both in dentistry and as a corrosion-resistant conductor of weak electrical signals in tool engineering. The work studies the kinetics of the disorder→order phase transformation in the Cu–56Au alloy, during which the disordered fcc lattice (A1-phase) is rearranged into an atomically ordered one with the L10 superstructure. The initial disordered state of the alloy was obtained in two ways: applying plastic deformation by 90 % or quenching at a temperature of above 600 °C (i. e., from the region of the A1-phase existence). To form the L10 superstructure, annealing was carried out at temperatures of 200, 225, and 250 °C. The annealing duration ranged from 1 h to 2 months. Resistometry was chosen as the main technique to study the kinetics of the disorder→order transformation. The temperature dependences of the electrical resistivity of the alloy in various structural states are obtained. The authors constructed the graphs of the electrical resistance dependence on the annealing time logarithm, based on which, the rate of the new phase formation was estimated. To evaluate the structural state of the alloy at various transformation stages, the authors used X-ray diffraction analysis (XRD). The crystal structure rearrangement during the transformation is shown by the example of splitting the initial cubic A1-phase peak (200) into two tetragonal ordered L10 phase peaks – (200) and (002). Based on the resistometry and X-ray diffraction analysis data, the authors carried out a quantitative assessment of the rate of the disorder→order phase transformation in the alloy under the study. It is established that the values of the converted volume fraction (resistometry) and the long-range order degree (X-ray diffraction analysis) are close. The study shows that in the temperature range of 200–250 °C, the rate of atomic ordering according to the L10 type in the nonstoichiometric alloy Cu–56 at. % Au is maximum at 250 °C. It is identified that the disorder→order transformation in the initially quenched specimens of the investigated alloy proceeds approximately an order of magnitude faster than in preliminarily deformed specimens

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Crucihimalaya himalaica is a close relative of Arabidopsis with typical Qinghai–Tibet Plateau (QTP) distribution. Here, by combining short- and long-read sequencing technologies, we provide a de novo genome sequence of C. himalaica. Our results suggest that the quick uplifting of the QTP coincided with the expansion of repeat elements. Gene families showing dramatic contractions and expansions, as well as genes showing clear signs of natural selection, were likely responsible for C. himalaica’s specific adaptation to the harsh environment of the QTP. We also show that the transition to self-pollination of C. himalaica might have enabled its occupation of the QTP. This study provides insights into how plants might adapt to extreme environmental conditions

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

Polyploidy plays an important role in evolution because it can lead to increased genetic complexity and speciation. It also provides an extra copy buffer and increases genetic novelty. While both common and well-studied in plants, polyploidy is rare in animals, and most polyploid animals reproduce asexually. Amphibians represent a dramatic vertebrate exception, with multiple independent sexually reproducing polyploid lineages, but very few cases have been studied in any detail. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful model animal polyploid system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on evolution of adaptation in animals

Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude

Crucihimalaya himalaica is a close relative of Arabidopsis with typical Qinghai--Tibet Plateau (QTP) distribution. Here, by combining short- and long-read sequencing technologies, we provide a de novo genome sequence of C. himalaica. Our results suggest that the quick uplifting of the QTP coincided with the expansion of repeat elements. Gene families showing dramatic contractions and expansions, as well as genes showing clear signs of natural selection, were likely responsible for C. himalaica"s specific adaptation to the harsh environment of the QTP. We also show that the transition to self-pollination of C. himalaica might have enabled its occupation of the QTP. This study provides insights into how plants might adapt to extreme environmental conditions

Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous

Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes.

A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here, we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to the establishment of allotetraploid Arabidopsis kamchatica. First, we provide chromosome-level genome assemblies for two self-fertilizing diploid A. lyrata accessions, one from North America and one from Siberia, including a fully assembled S-locus for the latter. We then propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, date this independent transition to ∼90 Kya, and infer evolutionary relationships between Siberian and North American A. lyrata, showing an independent transition to selfing in Siberia. Finally, we provide evidence that this selfing Siberian A. lyrata lineage contributed to the formation of the allotetraploid A. kamchatica and propose that the selfing of the latter is mediated by the loss-of-function mutation in a dominant S-allele inherited from A. lyrata

Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and wellstudied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals.S1 Text. Summary of cytogenetic observations and mechanisms for unidirectional introgression. (DOCX)S1 Table. Sample information, BioSample IDs, metadata, ploidy inference and filtering. (XLSX)S2 Table. Summary statistics for each of the species calculated with R package “PopGenome”. (XLSX)S3 Table. The average test AUC (area under the Receiving Operator Curve) for the replicate runs for all the species in MaxEnt modeling for predicting species distribution from climate data at the species occurrences. (XLSX)S4 Table. Instances of polyploid Neobatrachus. (XLSX)S1 Fig. Species tree and admixture results for optimal clustering at K equals 3, 7 and 9 (see S4 Fig. for optimal number of clusters). Vertical colored bars to the left of the tips of the tree correspond to our final species assignments (S1 Table); colors of the bars are species-specific and correspond to the branch colors from Fig 1A; filtered out samples are marked with black bars.S2 Fig. Nuclear species tree as inferred using ASTRAL, all nuclear loci, and complete taxon sampling. Figure extends across four parts (A, B, C, D) and is color coded by species identity.S3 Fig. Two dimensional representations of MDS gene tree space, colored by optimal clustering scheme for two dimensions (k = 2) and three dimensions (k = 4), and their associated topologies inferred using ASTRAL. Each point represents a single gene tree, colored clusters match colored trees displayed to the right. Nodes at values indicate bootstrap support.S4 Fig. Cross-validation plot showing three local optimal solutions for ADMIXTURE clustering at K equals 3, 7 and 9.S5 Fig. (A) Gene trees, colored by clade, for 361 nuclear loci based on 2 individuals per species show considerable incongruence and differ from the species trees (bold black topology). (B) Gene trees for diploid individuals only also show considerable incongruence and differ from the species trees (bold black topology). (C,D) Species tree colored by topological consistency as measured by gene concordance factors—gCF%, the percentage of loci which decisively favor a given bipartition. Warmer colors indicate high discordance, cooler colors indicate strong concordance.S6 Fig. Genealogies for six randomly sampled nuclear loci (y-axis) with different diploid individuals chosen as representatives for each species (different sample sets, x-axis) are consistent with each other. Genealogical conflict remains only among loci. This supports a scenario of rapid speciation of the diploid species without secondary contact or persistent incomplete lineage sorting.S7 Fig. Sequenced loci statistics on alignment length and number of variable sites inferred by AMAS (11).S8 Fig. Distribution of allele frequencies of biallelic sites in Neobatrachus tetraploids supports tetrasomic inheritance mode in N. sudellae and N. aquilonius and mixed inheritance mode in N. kunapalari. (A) Pairwise combination of individuals within the diploid species model the expected allele frequencies in autotetraploids with tetrasomic inheritance (blue line), when pairwise combination of individuals between the diploid Neobatrachus species model the expected distribution for allotetraploids with disomic inheritance mode (purple line). Modeled allotetraploids show excess of intermediate allele frequencies compared to autotetraploids. Gray area shows 95% confidence interval. (B) Comparing the ratio between intermediate (40–60%) and rare (<30%) allele frequencies we reject allotetraploid origin for N. sudellae and N. aquilonius, when N. kunapalari shows intermediate distribution, suggesting mixed inheritance. Comparisons performed with Wilcoxon tests adjusted for multiple testing.S9 Fig. SnaQ analysis. A. The optimum phylogenetic network includes two hybridization events. B. Network score has the best support at minumum 2 hybridization events, additional allowed hybridizations do not increase the network score.S10 Fig. Heatmap and hierarchical clustering of the Neobatrachus lineages based on the distance matrix from pairwise median Fst values. Tetraploid species (N. sudellae, N. aquilonius and N. kunapalari; highlighted with black left bar) cluster together and are characterised by the lowest Fst values between each other. This, together with low Fst values between tetraploid and diploid lineages, can probably be explained by the gene flow within the tetraploids and between the diploids and the tetraploids. Diploid lineages (highlighted with grey left bar) appear to be more isolated from each other compared to tetraploids, which is in agreement with ADMIXTURE assignment results and TreeMix estimations of possible migration events.S11 Fig. Occurrence data locations registered at the AmphibiaWeb database for Neobatrachus species: A—tetraploids, B—diploids.S12 Fig. PCA analysis of bioclimatic variables for Neobatrachus entries in the occurrence AmphibiaWeb database. A) Barplot showing the percentage of variances explained by each principal component. The first three principal components are labeled with the top three contributions of variables. BIO10 = Mean Temperature of Warmest Quarter, BIO12 = Annual Precipitation, BIO17 = Precipitation of Driest Quarter, BIO18 = Precipitation of Warmest Quarter, BIO19 = Precipitation of Coldest Quarter. B-D) Pairwise combinations of the first three principal components, where individuals with a similar profile of bioclimatic data are grouped together. Points represent each individual and colored according to the species assignment, ellipses represent 95% confidence area.S13 Fig. The results of the jackknife test of variable importance for models on each species. BIO19 (Precipitation of Coldest Quarter) was the most informative variable for the models of N. pelobatoides and N. albipes distributions; BIO18 (Precipitation of Warmest Quarter) was the most informative variable for the models of N. wilsmorei, N. sutor and N. kunapalari; BIO17 (Precipitation of Driest Quarter) was the most informative variable for the model of N. fulvus; BIO10 (Mean Temperature of Warmest Quarter) for N. pictus; and BIO9 (Mean Temperature of Driest Quarter) for N. sudellae and N. aquilonius.S14 Fig. The point-wise mean of the 10 models for each of the diploid species build on environmental layers from the current climate data and applied to the environmental layers from the Last Glacial Maximum climate data.S15 Fig. The point-wise mean of the 10 models for each of the tetraploid species build on environmental layers from the current climate data and applied to the environmental layers from the Last Glacial Maximum climate data.S16 Fig. Karyotypes of Neobatrachus. A) N. sutor [2n], B) N. pictus x N. sudellae triploid [3n] hybrid from Moyston, east of the Grampians, Victoria, C) N. fulvus x N. sutor triploid [3n] hybrid from Learmonth, Western Australia, D) N. sudellae [4n], E) tetraploid x tetraploid hybrid from north of Menzies, Western Australia, F) N. pictus x N. sudellae pentaploid [5n] hybrid from Moyston, east of the Grampians, Victoria. Arrowheads indicate nucleolar organiser regions (NORs).A Australian Research Council Discovery grant, postdoctoral fellowship from The Research Foundation – Flanders (FWO) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme.http://www.plosgenetics.orgam2021BiochemistryGeneticsMicrobiology and Plant Patholog