Testing the association of phenotypes with polyploidy: An example using herbaceous and woody eudicots

Karyotype evolution and speciation in Orthoptera

Karyotype evolution might fuel speciation and can thereby contribute to species diversity. To test the hypothesis that speciation and karyotype change are linked, we estimated anagenetic and cladogenetic rates of karyotype evolution as well as speciation rates in Orthoptera. We compiled the male diploid chromosome number and the number of visible chromosome arms (the fundamental number) from published sources for 1,541 species. Chromosome-associated speciation rates were estimated by jointly modelling cladogenetic and anagenetic character evolution and the phylogenetic birth-death process in a Bayesian statistical framework using a subset of 516 species from 14 families. Our findings unveiled heterogeneity among orthopteran families in the pace of karyotype evolution and whether it was linked to speciation. In 6/14 clades, we found evidence supporting speciation-associated (cladogenetic) karyotype changes, while in 6/14 clades karyotype evolution was primarily anagenetic. The remaining clades (2/14) showed uncertainty in favour of either model. We further analyzed whether flightless phenotype, and thus less mobile species, showed higher rates of karyotype evolution. We showed that the flightless phenotype is associated with the rate of chromosome loss. The finding indicates contrasting patterns of karyotype evolution within specific orthopteran lineages, thus emphasizing substantial diversity in the pace of this evolutionary process. It also implies that substantial changes in chromosome number, arising from instances of chromosomal gains and losses, are recurring events in orthopterans that are associated with reproductive isolation and speciation, at least in some groups.

Macroevolutionary inference of complex modes of chromosomal speciation in a cosmopolitan plant lineage

The effects of single chromosome number change-dysploidy - mediating diversification remain poorly understood. Dysploidy modifies recombination rates, linkage, or reproductive isolation, especially for one-fifth of all eukaryote lineages with holocentric chromosomes. Dysploidy effects on diversification have not been estimated because modeling chromosome numbers linked to diversification with heterogeneity along phylogenies is quantitatively challenging. We propose a new state-dependent diversification model of chromosome evolution that links diversification rates to dysploidy rates considering heterogeneity and differentiates between anagenetic and cladogenetic changes. We apply this model to Carex (Cyperaceae), a cosmopolitan flowering plant clade with holocentric chromosomes. We recover two distinct modes of chromosomal evolution and speciation in Carex. In one diversification mode, dysploidy occurs frequently and drives faster diversification rates. In the other mode, dysploidy is rare, and diversification is driven by hidden, unmeasured factors. When we use a model that excludes hidden states, we mistakenly infer a strong, uniformly positive effect of dysploidy on diversification, showing that standard models may lead to confident but incorrect conclusions about diversification. This study demonstrates that dysploidy can have a significant role in speciation in a large plant clade despite the presence of other unmeasured factors that simultaneously affect diversification.

Polyploidy linked with species richness but not diversification rates or niche breadth in Australian Pomaderreae (Rhamnaceae)

BACKGROUND AND AIMS

Polyploidy is an important evolutionary driver for plants and has been linked with higher species richness and increases in diversification rate. These correlations between ploidy and plant radiations could be the result of polyploid lineages exploiting broader niche space and novel niches due to their enhanced adaptability. The evolution of ploidy and its link to plant diversification across the Australian continent is not well understood. Here, we focus on the ploidy evolution of the Australasian Rhamnaceae tribe Pomaderreae.

METHODS

We generated a densely sampled phylogeny (90 %, 215/240 species) of the tribe and used it to test for the evolution of ploidy. We obtained 30 orthologous nuclear loci per sample and dated the phylogeny using treePL. Ploidy estimates for each sequenced species were obtained using nQuire, based on phased sequence data. We used MiSSE to obtain tip diversification rates and tested for significant relationships between diversification rates and ploidy. We also assessed for relationships between ploidy level and niche breadth, using distributional records, species distributional modelling and WorldClim data.

KEY RESULTS

Polyploidy is extensive across the tribe, with almost half (45 %) of species and the majority of genera exhibiting this trait. We found a significant positive relationship between polyploidy and genus size (i.e. species richness), but a non-significant positive relationship between polyploidy and diversification rates. Polyploidy did not result in significantly wider niche space occupancy for Pomaderreae; however, polyploidy did allow transitions into novel wetter niches. Spatially, eastern Australia is the diversification hotspot for Pomaderreae in contrast to the species hotspot of south-west Western Australia.

CONCLUSIONS

The relationship between polyploidy and diversification is complex. Ancient polyploidization events likely played an important role in the diversification of species-rich genera. A lag time effect may explain the uncoupling of tip diversification rates and polyploidy of extant lineages. Further studies on other groups are required to validate these hypotheses.

ChromEvol v.3: modeling rate heterogeneity in chromosome number evolution

Changes in chromosome numbers are a prominent driver of plant evolution, impacting ecological diversification, stress tolerance, and phenotypes. ChromEvol is a widely used software tool for deciphering patterns of chromosome-number change along a phylogeny of interest. It evaluates the fit of alternative models to the data, estimates transition rates of different types of events, and infers the expected number of events along each branch of the phylogeny. We introduce ChromEvol v.3, featuring multiple novel methodological advancements that capture variation in the transition rates along a phylogeny. This version better allows researchers to identify how dysploidy and polyploidy rates change based on the number of chromosomes in the genome, with respect to a discrete trait, or at certain subclades of the phylogeny. We demonstrate the applicability of the new models on the Solanaceae phylogeny. Our analyses identify four chromosome-number transition regimes that characterize distinct Solanaceae clades and demonstrate an association between self-compatibility and altered dynamics of chromosome-number evolution. ChromEvol v.3, available at https://github.com/anatshafir1/chromevol, offers researchers a more flexible, comprehensive, and accurate tool to investigate the evolution of chromosome numbers and the various processes affecting it.

Genomic correlates of vascular plant reproductive complexity and the uniqueness of angiosperms

Whole genome duplication (WGD) likely plays an important role in plant macroevolution, and has been implicated in diversification rate shifts, structural innovations, and increased disparity. But the general effects of WGD are challenging to evaluate, in part due to the difficulty of directly comparing morphological patterns across disparate clades. We explored relationships between WGD and the evolution of reproductive complexity across vascular plants using a metric based on the number of reproductive part types. We used multiple regression models to evaluate the relative importance of inferred WGD events, genome size, and a suite of additional variables relating to growth habit and reproductive biology in explaining part type complexity. WGD was a consistent predictor of reproductive complexity only among angiosperms. Across vascular plants generally, reproductive biology, clade identity, and the presence of bisexual strobili (those that produce microsporangiate and megasporangiate organs) were better predictors of complexity. Angiosperms are unique among vascular plants in combining frequent polyploidy with high-reproductive complexity. Whether WGD is mechanistically linked to floral complexity is unclear, but we suggest widespread polyploidy and increased complexity were ultimately facilitated by the evolution of herbaceous growth habits in early angiosperms.

New beginnings for dead ends: polyploidy, -SSE models and the dead-end hypothesis

BACKGROUND

Since the mid-20th century, it has been argued by some that the transition from diploidy to polyploidy is an 'evolutionary dead end' in plants. Although this point has been debated ever since, multiple definitions of 'dead end' have been used in the polyploidy literature, without sufficient differentiation between alternative uses.

SCOPE

Here, we focus on the two most common conceptions of the dead-end hypothesis currently discussed: the 'lowering diversification' hypothesis and the 'rarely successful' hypothesis. We discuss the evidence for both hypotheses, and we use a recently developed method of inferring tip diversification rates to demonstrate tests for the effect of ploidy on diversification in Solanaceae.

CONCLUSIONS

We find that diversification rates in the family are not strongly correlated with ploidy or with the closely related trait of breeding system. We also outline recent work in the field that moves beyond the relatively simple question of whether polyploidy increases, decreases or does not significantly affect diversification rates in plants.

From Micro to Macro: Avian Chromosome Evolution is Dominated by Natural Selection

Birds display striking variation in chromosome number, defying the traditional view of highly conserved avian karyotypes. However, the evolutionary drivers of this variability remain unclear. To address this, we fit probabilistic models of chromosome number evolution across birds, enabling us to estimate rates of evolution for total chromosome number and the number of microchromosomes and macrochromosomes while simultaneously accounting for the impact of other evolving traits. Our analyses revealed higher rates of chromosome fusion than fission across all bird lineages. Notably, much of this signal was driven by Passeriformes, where migratory species showed a particularly strong bias towards fusions compared to sedentary counterparts. Furthermore, a robust correlation between the rearrangement rates of microchromosomes and macrochromosomes suggests that genome-wide processes drive rates of structural evolution. Additionally, we found that lineages with larger population sizes exhibited higher rates of both fusion and fission, indicating that positive selection plays a dominant role in driving divergence in chromosome number. Our findings illuminate the evolutionary dynamics of avian karyotypes and highlight that, while the fitness effects of random structural mutations are often deleterious, beneficial mutations may dominate karyotype divergence in some clades.

Can ploidy levels explain the variation of Herbertia lahue (Iridaceae)?

Polyploidy is often related with phenotypic variation, as observed in Herbertia lahue, a geophyte species. This study examined the H. lahue polyploid series and departure in cytogenetic, morphometric, and pollen data. Diploids (2n=2x=14) present bimodal karyotype with two long and five short chromosome pairs, while hexaploids (2n=6x=42) and octoploids (2n=8x=56) present a gradual decrease in chromosome size. All cytotypes have CMA+/DAPI- bands co-localized with 18S rDNA sites in the satellite region (no DAPI+ bands in any cytotype). Unlike diploids and octoploids, 5S rDNA interstitial sites in hexaploids are not in a syntenic position with 18S rDNA sites. Genome size is effective as an indirect predictor of the cytotypes since 2C-values increased according to ploidy level. The reduction in the number of the rDNA sites in polyploids associated with their lower 1Cx-values compared to diploids may suggest a genome downsizing process. Morphometric analysis revealed significant differences among cytotypes, and discriminant analysis identified three morphometric groupings corresponding to the cytotypes. The phenotypic variation observed in pollen grains, bulbs, and ovary characters suggested the gigas effect. Concluding, remarkable differentiation was observed at both genomic and phenotypic characters in all the cytotypes analyzed, suggesting a possible ongoing speciation process in H. lahue.

The global distribution of angiosperm genome size is shaped by climate

Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.

Drivers of diversification in Linum (Linaceae) by means of chromosome evolution: correlations with biogeography, breeding system and habit

BACKGROUND AND AIMS

Chromosome evolution leads to hybrid dysfunction and recombination patterns and has thus been proposed as a major driver of diversification in all branches of the tree of life, including flowering plants. In this study we used the genus Linum (flax species) to evaluate the effects of chromosomal evolution on diversification rates and on traits that are important for sexual reproduction. Linum is a useful study group because it has considerable reproductive polymorphism (heterostyly) and chromosomal variation (n = 6-36) and a complex pattern of biogeographical distribution.

METHODS

We tested several traditional hypotheses of chromosomal evolution. We analysed changes in chromosome number across the phylogenetic tree (ChromEvol model) in combination with diversification rates (ChromoSSE model), biogeographical distribution, heterostyly and habit (ChromePlus model).

KEY RESULTS

Chromosome number evolved across the Linum phylogeny from an estimated ancestral chromosome number of n = 9. While there were few apparent incidences of cladogenesis through chromosome evolution, we inferred up to five chromosomal speciation events. Chromosome evolution was not related to heterostyly but did show significant relationships with habit and geographical range. Polyploidy was negatively correlated with perennial habit, as expected from the relative commonness of perennial woodiness and absence of perennial clonality in the genus. The colonization of new areas was linked to genome rearrangements (polyploidy and dysploidy), which could be associated with speciation events during the colonization process.

CONCLUSIONS

Chromosome evolution is a key trait in some clades of the Linum phylogeny. Chromosome evolution directly impacts speciation and indirectly influences biogeographical processes and important plant traits.

Incidence and evolutionary relevance of autotriploid cytotypes in a relict member of the genus Daphne (Thymelaeaceae)

Odd ploidy-level cytotypes in sexually reproducing species are considered a dead end due to absent or reduced fertility. If sterility is only partial, however, their contribution to the population gene pool can be augmented by longevity and clonal growth. To test this, we investigated the cytotype origin and spatial pattern, and pollen viability in three relict shrub species of the genus Daphne (Thymelaeaceae Juss.) in central Europe. Daphne cneorum subsp. cneorum is a widespread European species that has a broad ecological amplitude, whereas D. cneorum subsp. arbusculoides and D. arbuscula are narrow endemics of the western Pannonian Plain and the Western Carpathians, respectively. Our study confirmed that all three taxa are diploid. However, of more than a thousand analysed individuals of D. cneorum subsp. cneorum, five in four different populations were triploid. Our data indicate that these triploids most likely originate from recurrent autopolyploidization events caused by the fusion of reduced and unreduced gametes. High pollen viability was observed in all three taxa and in both diploid and triploid cytotypes, ranging from 65 to 100 %. Our study highlights the significant role of odd ploidy-level cytotypes in interploidy gene flow, calling for more research into their reproduction, genetic variability, and overall fitness. Interestingly, while the endemic D. arbuscula differs from D. cneorum based on genetic and genome size data, D. cneorum subsp. arbusculoides was indistinguishable from D. cneorum subsp. cneorum. However, our study reveals that the subspecies differ in the number of flowers per inflorescence. This is the first comprehensive cytogeographic study of this intriguing genus at a regional scale, and in spite of its karyological stability, it contributes to our understanding of genomic evolution in plant species with a wide ecological amplitude.

A non-homogeneous model of chromosome-number evolution to reveal shifts in the transition patterns across the phylogeny

Changes in chromosome numbers, including polyploidy and dysploidy events, play a key role in eukaryote evolution as they could expediate reproductive isolation and have the potential to foster phenotypic diversification. Deciphering the pattern of chromosome-number change within a phylogeny currently relies on probabilistic evolutionary models. All currently available models assume time homogeneity, such that the transition rates are identical throughout the phylogeny. Here, we develop heterogeneous models of chromosome-number evolution that allow multiple transition regimes to operate in distinct parts of the phylogeny. The partition of the phylogeny to distinct transition regimes may be specified by the researcher or, alternatively, identified using a sequential testing approach. Once the number and locations of shifts in the transition pattern are determined, a second search phase identifies regimes with similar transition dynamics, which could indicate on convergent evolution. Using simulations, we study the performance of the developed model to detect shifts in patterns of chromosome-number evolution and demonstrate its applicability by analyzing the evolution of chromosome numbers within the Cyperaceae plant family. The developed model extends the capabilities of probabilistic models of chromosome-number evolution and should be particularly helpful for the analyses of large phylogenies that include multiple distinct subclades.

The Chromosome Counts Database (CCDB)

For decades, plant biologists have been interested in the determination and documentation of chromosome numbers for extant taxa. This central cytological character has been used as an important phylogenetic marker and as an indicator for major genomic events such as polyploidy and dysploidy. Due to their significance and the relative ease by which chromosome numbers can be obtained, chromosome numbers have been extensively recorded across the plant kingdom and documented in a wide variety of resources. This makes the collection process a wearing task, often leading to partial data retrieval. In 2015, the Chromosome Counts Database (CCDB) was assembled, being an online unified community resource. This database compiles dozens of different chromosome counts sources, of which a significant portion had been unavailable before in a digitized, searchable format. The vast amount of data assembled in CCDB has already enabled a large number of analyses to examine the evolution of different plant hierarchies, as well as the application of various follow-up analyses, such as ploidy-level inference using chromEvol. CCDB ( http://ccdb.tau.ac.il/ ) encourages data sharing among the botanical community and is expected to continue expanding as additional chromosome numbers are recorded.

Using ChromEvol to Determine the Mode of Chromosomal Evolution

The ChromEvol software was the first to implement a likelihood-based approach, using probabilistic models that depict the pattern of chromosome number change along a specified phylogeny. The initial models have been completed and expanded during the last years. New parameters that model polyploid chromosome evolution have been implemented in ChromEvol v.2. In recent years, new and more complex models have been developed. The BiChrom model is able to implement two distinct chromosome models for the two possible trait states of a binary character of interest. ChromoSSE jointly implements chromosome evolution, speciation, and extinction. In the near future, we will be able to study chromosome evolution with increasingly complex models.

The relevance of chromosome fissions for major ribosomal DNA dispersion in hymenopteran insects

Ribosomal DNA (rDNA) loci are essential for cellular metabolism due to their participation in ribosome biogenesis. Although these genes have been widely cytogenetically mapped, the evolutionary mechanisms behind their variability in number and chromosomal location remain elusive, even in well-known biological groups, such as ants, bees and wasps (Insecta: Hymenoptera). To address this question in Hymenoptera and therefore advance the understanding of rDNA evolution in insects in general, we integrated molecular cytogenetic data, a phylogenomic framework, model-based predictions and genome sequencing. Hence, we assessed the main evolutionary trends shaping the chromosomal distribution of rDNA loci in Hymenoptera. We noticed the conservation of one site of rDNA per haploid genome, suggesting that a single 45S rDNA locus is the putative ancestral pattern for aculeate Hymenoptera. Moreover, our results highlighted a nonrandom distribution of rDNA in Hymenoptera karyotypes, as well as a lineage-specific preferential location. The proximal location of rDNA is favoured in species with multiple loci and in the two families of Hymenoptera that show the highest range of chromosome numbers: Formicidae and Vespidae. We propose that chromosome fissions have played a crucial role in the distribution pattern of rDNA loci through the evolutionary diversification of Hymenoptera. Moreover, our genomic analysis of two species, one with a single locus of rDNA and one with multiple loci, supported that loci multiplication is followed by sequence divergence. Our results provide detailed information about the number and chromosomal position of rDNA in Hymenoptera and, therefore, broaden our knowledge regarding rDNA evolutionary dynamics in insects.

Model adequacy tests for probabilistic models of chromosome-number evolution

Chromosome number is a central feature of eukaryote genomes. Deciphering patterns of chromosome-number change along a phylogeny is central to the inference of whole genome duplications and ancestral chromosome numbers. ChromEvol is a probabilistic inference tool that allows the evaluation of several models of chromosome-number evolution and their fit to the data. However, fitting a model does not necessarily mean that the model describes the empirical data adequately. This vulnerability may lead to incorrect conclusions when model assumptions are not met by real data. Here, we present a model adequacy test for likelihood models of chromosome-number evolution. The procedure allows us to determine whether the model can generate data with similar characteristics as those found in the observed ones. We demonstrate that using inadequate models can lead to inflated errors in several inference tasks. Applying the developed method to 200 angiosperm genera, we find that in many of these, the best-fitting model provides poor fit to the data. The inadequacy rate increases in large clades or in those in which hybridizations are present. The developed model adequacy test can help researchers to identify phylogenies whose underlying evolutionary patterns deviate substantially from current modelling assumptions and should guide future methods development.

Evolutionary dynamics of genome size in a radiation of woody plants

PREMISE

Plant genome size ranges widely, providing many opportunities to examine how genome size variation affects plant form and function. We analyzed trends in chromosome number, genome size, and leaf traits for the woody angiosperm clade Viburnum to examine the evolutionary associations, functional implications, and possible drivers of genome size.

METHODS

Chromosome counts and genome size estimates were mapped onto a Viburnum phylogeny to infer the location and frequency of polyploidization events and trends in genome size evolution. Genome size was analyzed with leaf anatomical and physiological data to evaluate the influence of genome size on plant function.

RESULTS

We discovered nine independent polyploidization events, two reductions in base chromosome number, and substantial variation in genome size with a slight trend toward genome size reduction in polyploids. We did not find strong relationships between genome size and the functional and morphological traits that have been highlighted at broader phylogenetic scales.

CONCLUSIONS

Polyploidization events were sometimes associated with rapid radiations, demonstrating that polyploid lineages can be highly successful. Relationships between genome size and plant physiological function observed at broad phylogenetic scales may be largely irrelevant to the evolutionary dynamics of genome size at smaller scales. The view that plants readily tolerate changes in ploidy and genome size, and often do so, appears to apply to Viburnum.

The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches

Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.

Chromosome number evolves at equal rates in holocentric and monocentric clades

Despite the fundamental role of centromeres two different types are observed across plants and animals. Monocentric chromosomes possess a single region that function as the centromere while in holocentric chromosomes centromere activity is spread across the entire chromosome. Proper segregation may fail in species with monocentric chromosomes after a fusion or fission, which may lead to chromosomes with no centromere or multiple centromeres. In contrast, species with holocentric chromosomes should still be able to safely segregate chromosomes after fusion or fission. This along with the observation of high chromosome number in some holocentric clades has led to the hypothesis that holocentricity leads to higher rates of chromosome number evolution. To test for differences in rates of chromosome number evolution between these systems, we analyzed data from 4,393 species of insects in a phylogenetic framework. We found that insect orders exhibit striking differences in rates of fissions, fusions, and polyploidy. However, across all insects we found no evidence that holocentric clades have higher rates of fissions, fusions, or polyploidy than monocentric clades. Our results suggest that holocentricity alone does not lead to higher rates of chromosome number changes. Instead, we suggest that other co-evolving traits must explain striking differences between clades.

Lineage-specific patterns of chromosome evolution are the rule not the exception in Polyneoptera insects

The structure of a genome can be described at its simplest by the number of chromosomes and the sex chromosome system it contains. Despite over a century of study, the evolution of genome structure on this scale remains recalcitrant to broad generalizations that can be applied across clades. To address this issue, we have assembled a dataset of 823 karyotypes from the insect group Polyneoptera. This group contains orders with a range of variations in chromosome number, and offer the opportunity to explore the possible causes of these differences. We have analysed these data using both phylogenetic and taxonomic approaches. Our analysis allows us to assess the importance of rates of evolution, phylogenetic history, sex chromosome systems, parthenogenesis and genome size on variation in chromosome number within clades. We find that fusions play a key role in the origin of new sex chromosomes, and that orders exhibit striking differences in rates of fusions, fissions and polyploidy. Our results suggest that the difficulty in finding consistent rules that govern evolution at this scale may be due to the presence of many interacting forces that can lead to variation among groups.

Has the Polyploid Wave Ebbed?

There was a wave of whole genome duplications (WGD) during and subsequent to the K-Pg interface, which was followed by an increase in the proportion of species that were polyploid. I consider why this wave of polyploid speciation has continued to rise through the divergent evolution of polyploid lineages, and through rounds of homoploid and heteroploid chromosomal change. I also consider why the polyploid speciation wave is likely to rise in the next millennium. I propose that the speed of polyploid genesis through ploidal increase and through diversification among polyploids likely will be greater than the speed of diploid speciation. The increase in polyploid diversity is expected to lag well behind episodes of WGD, owing to the very long period required for species diversification either by lineage splitting or additional rounds of polyploidy, in addition to the long period of genomic adjustment to higher ploidal levels in neopolyploids.

Interaction among ploidy, breeding system and lineage diversification

If particular traits consistently affect rates of speciation and extinction, broad macroevolutionary patterns can be interpreted as consequences of selection at high levels of the biological hierarchy. Identifying traits associated with diversification rates is difficult because of the wide variety of characters under consideration and the statistical challenges of testing for associations from comparative phylogenetic data. Ploidy (diploid vs polyploid states) and breeding system (self-incompatible vs self-compatible states) are both thought to be drivers of differential diversification in angiosperms. We fit 29 diversification models to extensive trait and phylogenetic data in Solanaceae and investigate how speciation and extinction rate differences are associated with ploidy, breeding system, and the interaction between these traits. We show that diversification patterns in Solanaceae are better explained by breeding system and an additional unobserved factor, rather than by ploidy. We also find that the most common evolutionary pathway to polyploidy in Solanaceae occurs via direct breakdown of self-incompatibility by whole genome duplication, rather than indirectly via breakdown followed by polyploidization. Comparing multiple stochastic diversification models that include complex trait interactions alongside hidden states enhances our understanding of the macroevolutionary patterns in plant phylogenies.

Evolutionary associations between polyploidy, clonal reproduction, and perenniality in the angiosperms

Clonal reproduction is thought to facilitate polyploid establishment in the angiosperms, but the evolutionary relationship between polyploidy and clonality has not been thoroughly tested. A perennial life history may confer many of the same advantages, and the relative importance of clonality versus perenniality is unknown. We used phylogenetic comparative analyses of 1751 species to examine associations between polyploidy, clonality, and life history. We test hypotheses of co-evolution by determining the sequence of trait development. Polyploidy is associated with both clonality and perenniality across species, and analyses show that clonality can be an important predictor of polyploidy beyond perenniality. Tests of directionality on our full dataset suggest that polyploidy is more likely to promote clonality or perenniality than vice versa, although there are significant differences in patterns of co-evolution among major angiosperm groups. Our results suggest that polyploidy and clonal reproduction are evolutionarily associated across the angiosperms, even when perenniality is considered, but we find little evidence at the whole-angiosperm level for the hypothesis that clonality promotes polyploidy. However, variation among different clades indicates that polyploidy and clonality are interacting in diverse ways, likely to be due to the variable roles of clonality in their evolutionary histories.

Meiotic drive shapes rates of karyotype evolution in mammals

Chromosome number is perhaps the most basic characteristic of a genome, yet generalizations that can explain the evolution of this trait across large clades have remained elusive. Using karyotype data from over 1000 mammals, we developed and applied a phylogenetic model of chromosome evolution that links chromosome number changes with karyotype morphology. Using our model, we infer that rates of chromosome number evolution are significantly lower in species with karyotypes that consist of either all bibrachial or all monobrachial chromosomes than in species with a mix of both types of morphologies. We suggest that species with homogeneous karyotypes may represent cases where meiotic drive acts to stabilize the karyotype, favoring the chromosome morphologies already present in the genome. In contrast, rapid bouts of chromosome number evolution in taxa with mixed karyotypes may indicate that a switch in the polarity of female meiotic drive favors changes in chromosome number. We do not find any evidence that karyotype morphology affects rates of speciation or extinction. Furthermore, we document that switches in meiotic drive polarity are likely common and have occurred in most major clades of mammals, and that rapid remodeling of karyotypes may be more common than once thought.

EyeChrom and CCDBcurator: Visualizing chromosome count data from plants

PREMISE OF THE STUDY

Chromosome count data are available for hundreds of plant species and can be explored in text-only format at the Chromosome Counts Database (http://ccdb.tau.ac.il). CCDBcurator and EyeChrom are an R package and a web application, respectively, that first curate and then visualize these data graphically, so that intra- and interspecific variation of chromosome numbers can be easily summarized and displayed for a given genus.

METHODS AND RESULTS

We developed R code to clean, summarize, and display in several formats the chromosome count data for a selected genus or set of species present in the Chromosome Counts Database. These data and figures can be exported for use in analyses, publications, or teaching.

CONCLUSIONS

Chromosome count data are critical for a number of evolutionary studies in plant biology, and their importance is underscored by the increasing appreciation of the prevalence of polyploidy in land plants. CCDBcurator and EyeChrom provide a fast, easy, and reproducible means of cleaning, curating, and then visualizing the chromosome count data currently available for plants.

chromploid: An R package for chromosome number evolution across the plant tree of life

PREMISE OF THE STUDY

Polyploidy has profound evolutionary consequences for land plants. Despite the availability of large phylogenetic and chromosomal data sets, estimating the rates of polyploidy and chromosomal evolution across the tree of life remains a challenging, computationally complex problem. We introduce the R package chromploid, which allows scientists to perform inference of chromosomal evolution rates across large phylogenetic trees.

METHODS AND RESULTS

chromploid is an open-source package in the R environment that calculates the likelihood function of models of chromosome evolution. Models of discrete character evolution can be customized using chromploid. We demonstrate the performance of the BiChroM model, testing for associations between rates of chromosome doubling (as a proxy for polyploidy) and a binary phenotypic character, within chromploid using simulations and empirical data from Solanum. In simulations, estimated chromosome-doubling rates were unbiased and the variance decreased with larger trees, but distinguishing small differences in rates of chromosome doubling, even from large data sets, remains challenging. In the Solanum data set, a custom model of chromosome number evolution demonstrated higher rates of chromosome doubling in herbaceous species compared to woody.

CONCLUSIONS

chromploid enables researchers to perform robust likelihood-based inferences using complex models of chromosome number evolution across large phylogenies.