the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.

Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing, disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution. Expected final online publication date for the Annual Review of Plant Biology, Volume 72 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

SummaryWhole genome duplication is considered to be a significant contributor to angiosperm speciation due to accumulation of rapid, strong interploid reproductive isolation. However, recent work suggests that interploid reproductive isolation may not be complete, especially among higher order cytotypes. This study evaluates postzygotic reproductive isolation among three cytotypes within a polyploid complex.We conducted reciprocal crosses using two diploid and two hexaploid populations each crossed to tetraploid populations spanning the geographic and phylogenetic range of the Campanula rotundifolia polyploid complex. Interploid and intrapopulation crosses were scored for fruit set, seed number, germination proportion and pollen viability. Postzygotic isolation was calculated for each cross as the product of these fitness components. A subset of offspring was cytotyped via flow cytometry.Postzygotic isolation was significantly lower in tetraploid-hexaploid crosses than diploid-tetraploid crosses, mostly due to substantially higher germination among tetraploid-hexaploid crosses. Tetraploid-hexaploid crosses produced pentaploids exclusively, whereas diploid-tetraploid crosses produced both triploids and tetraploids in high frequencies.Postzygotic isolation was weaker among higher order polyploids than between diploids and tetraploids, and unreduced gametes may facilitate diploid-tetraploid reproduction. This incomplete postzygotic isolation could allow ongoing interploid gene flow, especially among higher order polyploids, which may slow divergence and speciation in polyploid complexes.

Premise Whole‐genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. Methods Phylo‐transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. Results Well‐supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae‐specific WGD event Th‐ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well‐supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. Conclusions Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.

Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants.For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. However, while its sister family, Cleomaceae, has also been characterized by a WGD, its placement, as well as that of other WGD events in other families in the order, remains unclear. Using phylo-transcriptomics from 74 taxa and genome survey sequencing for 66 of those taxa, we infer nuclear and chloroplast phylogenies to assess relationships among the major families of the Brassicales and within the Brassicaceae. We then use multiple methods of WGD inference to assess placement of WGD events. We not only present well-supported chloroplast and nuclear phylogenies for the Brassicales, but we also putatively place Th-ɑ and provide evidence for previously unknown events, including one shared by at least two members of the Resedaceae, which we name Rs-ɑ. Given its economic importance and many genomic resources, the Brassicales are an ideal group to continue assessing WGD inference methods. We add to the current conversation on WGD inference difficulties, by demonstrating that sampling is especially important for WGD identification. 5

Premise Of The StudyBoth intrinsic and extrinsic factors contribute to a species distribution. Among plants, the extrinsic effects of glaciation and intrinsic effects of whole genome duplication are powerful drivers of biogeographical patterns, but the interplay of these factors is poorly understood. Here, we investigate the roles glaciation and whole‐genome duplication have played in the evolution of the widespread polyploid complex Campanula rotundifolia.MethodsWe assessed the cytotype of 37 populations that spanned the geographic and cytotypic range of the C. rotundifolia complex. We constructed a chloroplast phylogeny for these populations and used RAD‐seq to create nuclear phylogenies and networks for a subset of 23 populations; and estimated divergence times of major clades using Bayesian estimation of substitution rates.Key ResultsCampanula rotundifolia originated in south‐central Europe and underwent range expansion throughout much of Europe and North America. Multiple genome duplications have occurred in C. rotundifolia—at least two tetraploid and three hexaploid formations.ConclusionsNuclear and chloroplast phylogenies are largely congruent with a history of populations surviving glacial maxima in known Pleistocene refugia in Europe and North America. Divergent European clades are consistent with two disjunct glacial refugia within Europe. North America was colonized by hexaploids derived from Western European lineages. A glacial refugium in Midwestern North America likely facilitated post‐glacial recolonization of North America and limited genetic divergence. These results implicate both glaciation and whole‐genome duplication as contributing factors to the extant biogeography of C. rotundifolia.

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When differentiated lineages come into contact, their fates depend on demographic and reproductive factors. These factors have been well-studied in taxa of the same ploidy, but less is known about sympatric lineages that differ in ploidy, particularly with respect to demographic factors. We assessed prezygotic, postzygotic, and total reproductive isolation in naturally pollinated arrays of diploid-tetraploid and tetraploid-hexaploid population mixes of Campanula rotundifolia by measuring pollinator transitions, seed yield, germination rate, and proportion of hybrid offspring. Four frequencies of each cytotype were tested, and pollinators consistently overvisited rare cytotypes. Seed yield and F1 hybrid production were greater in 4X-6X arrays than 2X-4X arrays, whereas germination rates were similar, creating two distinct patterns of reproductive isolation. In 2X-4X arrays, postzygotic isolation was near complete (3% hybrid offspring), and prezygotic isolation associated with pollinator preference is expected to facilitate the persistence of minority cytotypes. However, in 4X-6X arrays where postzygotic isolation permitted hybrid formation (44% hybrids), pollinator behavior drove patterns of reproductive isolation, with rare cytotypes being more isolated and greater gene flow expected from rare into common cytotypes. In polyploid complexes, both the specific cytotypes in contact and local cytotype frequency, likely reflecting spatial demography, will influence likelihood of gene exchange.