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• 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.

The spectacular variation in species forms and richness across space and time can be explored using sophisticated and powerful tools recently developed by evolutionary modellers. In this contribution, we ask if the classic ‘Simpsonian’ view of tachytelic (fast), horotelic (standard) and bradytelic (slow) diversification rates can be distinguished with currently available tools and data. A neglected topic here is the role that the uncertainty of diversification rate estimates plays, where the lack of in‐depth uncertainty measures could hinder our ability to confidently suggest differences in speciation or extinction rates in any given comparison. We propose quantifying the relative uncertainty of diversification estimates, to better compare diversification tempo across phylogenies of different sizes and ages. We present three case studies, using the most popular models for diversification rate estimation, with or without fossils, to investigate claims of bradytely or tachytely. Using summary statistics and linear models, we ask if point estimates of diversification rates are comparable across clades. More specifically, we fit a linear model to understand which phylogenetic tree properties (including size and age) may affect the uncertainty of diversification estimates. We found the ‘Goldilocks of uncertainty’: Phylogenies that are young with insufficient tips or that are old increase the uncertainty of diversification estimates. The choice of diversification modelling approach is independent of the pattern of diversification rates decaying exponentially with clade age. In practice, we still cannot confidently compare diversification rates or their variation, due to uncertainties stemming from clade age, sample size and biased sampling. We emphasize the need for researchers to focus on estimating and presenting uncertainty in their estimates. Such uncertainty estimates are currently absent from many publications, limiting our ability to compare the tempo of diversifications across the tree of life. We conclude by proposing solutions and guidelines to encourage new studies for measure uncertainty. Resumen La variación espectacular en las formas y riqueza de las especies a través del tiempo y el espacio es estudiada por investigadores en el área de Evolución utilizando modelos sofisticados con modernas herramientas de software. En esta contribución, nos enfocamos en entender si la propuesta clásica de Simpson para la diversificación ya sea tachitélica (rápida) o braditélica (lenta) puede ser inferida utilizando los métodos actuales. Sin una medida de incertidumbre en los estimadores de la diversificación es imposible encontrar diferencias en los modos y tiempos evolutivos como lo propuso Simpson. Proponemos una medida relativa de incertidumbre para comparar estimadores de diversificación a través de clados con distintas edades y tamaños. Utilizando tres meta análisis que incluyen estudios de diversificación bajo los modelos más populares (con o sin el uso de fósiles), investigamos si los argumentos de braditelia y tachitelia son posibles. Adicionalmente, utilizamos estadísticas resumen y modelos lineales para entender si los estimadores de la diversificación son comparables. Uno de los modelos lineales que presentamos se enfoca en estimar la correlación de las propiedades de las filogenias con la incertidumbre de los estimadores de diversificación. Encontramos a la ‘Ricitos de Oro de la incertidumbre’ una propiedad de las filogenias en donde árboles muy pequeños y jóvenes, o árboles muy antiguos incrementan la incertidumbre de los estimadores de diversificación. Además, encontramos que la selección del modelo para estimar la diversificación no cambia el patrón de caída exponencial de las tasas de diversificación cuando se comparan contra la edad de los clados. Los orígenes de la incertidumbre en los estimadores que incluyen la edad de los clados y los sesgos en la muestra demuestran que aún no podemos comparar con confianza las tasas de diversificación en el árbol de la vida. Enfatizamos que los investigadores necesitan enfocarse en estimar y presentar medidas de incertidumbre para sus estimadores. Al no medir la incertidumbre no podemos comparar el tiempo de las diversificaciones en el árbol de la vida. Concluimos proponiendo soluciones y lineamientos para mejorar la presentación de la incertidumbre en estudios futuros.

Premise Competition from naturalized species and habitat loss are common threats to native biodiversity and may act synergistically to increase competition for decreasing habitat availability. We use Hawaiian dryland ferns as a model for the interactions between land‐use change and competition from naturalized species in determining habitat availability. Methods We used fine‐resolution climatic variables and carefully curated occurrence data from herbaria and community science repositories to estimate the distributions of Hawaiian dryland ferns. We quantified the degree to which naturalized ferns tend to occupy areas suitable for native species and mapped the remaining available habitat given land‐use change. Results Of all native species, Doryopteris angelica had the lowest percentage of occurrences of naturalized species in its suitable area while D. decora had the highest. However, all Doryopteris spp. had a higher percentage overlap, while Pellaea ternifolia had a lower percentage overlap, than expected by chance. Doryopteris decora and D. decipiens had the lowest proportions (<20%) of suitable area covering native habitat. Discussion Areas characterized by shared environmental preferences of native and naturalized ferns may decrease due to human development and fallowed agricultural lands. Our study demonstrates the value of place‐based application of a recently developed correlative ecological niche modeling approach for conservation risk assessment in a rapidly changing and urbanized island ecosystem. Hōʻuluʻulu manaʻo Hoʻolauna ʻO ka hoʻokūkū ma waena o nā lāhulu kūlohelohe a me ke emi ʻana o ke kaianoho he mau mea hoʻoweliweli maʻamau i nā meaola likeʻole (ke kūlohelohe a me ka ʻāpaʻakuma). I kekahi manawa, e kuahui like lākou i kēia hoʻokūkū a ʻuʻuku mai nō ka loaʻa ʻana o ka nohona. Ua hoʻomōhala mākou i kahi kaʻina hana me ka hoʻohana ʻana i nā ʻōkupukupu ʻāina maloʻo Hawaiʻi ma ke ʻano he kumu hoʻohālike no ke kūkaʻi ma waena o ka hoʻololi ʻana i ka ʻāina a me ka hoʻokūkū kūlohelohe i ke kaianoho ʻana i kahi noho kūpono no nā lāhulu ʻōiwi. Kiʻina Hana Ua hoʻohana mākou i nā lolelua aniau miomio o kekahi palapala ʻāina o kona ʻike ʻia ʻana mai nā waihona mea ulu a me nā waihona ʻepekema kaiāulu e hoʻokohu i ka nui o ka māhele ʻana o nā ʻōkupukupu ʻāina maloʻo Hawaiʻi. Helu ʻia ka nui kēkēlē o ko lākou noho ʻana ma kahi wahi noho kūpono like. Ma hope, palapala ʻāina ʻia ke koena o ke kaianoho i loaʻa i loko o ka hoʻololi ʻana i ka hoʻohana ʻāina ma Hawaiʻi. Hopena ʻOi aʻe ka hāiki o nā wahi noho kūpono i koho ʻia no nā lāʻau ʻāpaʻakuma ʻo Doryopteris ma mua o nā lāʻau ʻōiwi akā ʻaʻole ma mua o ka lāʻau ʻāpaʻakuma ʻo Pellaea ternifolia. Ma waena o nā ʻano ʻōiwi āpau, ʻo Doryopteris angelica ka haʻahaʻa loa o kona ʻike ʻia ʻana o nā ʻano kūlohelohe i kona kaianoho koho i manaʻo ʻia ʻoiai ʻo D. decora ka mea kiʻekiʻe loa. No D. decora a me D. decipiens ka lakio like haʻahaʻa loa (<20%) o nā wahi kūpono i manaʻo ʻia e uhi ana i ka nohona ʻōiwi. Kālaimanaʻo E emi ana paha nā māhele ʻāina i kohu pono i ka makemake o nā ʻōkupukupu ʻōiwi a me kūlohelohe ma muli o ka ʻōkomo kanaka a me ka mahi. Hōʻike ʻia ka waiwai o ka palapala ʻāina i haku ʻia iho nei ma kā mākou noiʻi ma ke ʻano he kumu hoʻohālikelike no ke ana ʻana i nā mea e hoʻoweliweli ana i nā kumu waiwai e loli wiki ana i loko o ka nohona e hoʻokiwikā ʻia nei ma loko o ke kaiaola mokupuni.

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.

Although numerous studies have surveyed the frequency with which different plant characters are associated with polyploidy, few statistical tools are available to identify the factors that potentially facilitate polyploidy. We describe a new probabilistic model, BiChroM, designed to associate the frequency of polyploidy and chromosomal change with a binary phenotypic character in a phylogeny. BiChroM provides a robust statistical framework for testing differences in rates of polyploidy associated with phenotypic characters along a phylogeny while simultaneously allowing for evolutionary transitions between character states. We used BiChroM to test whether polyploidy is more frequent in woody or herbaceous plants, based on tree with 4711 eudicot species. Although polyploidy occurs in woody species, rates of chromosome doubling were over six times higher in herbaceous species. Rates of single chromosome increases or decreases were also far higher in herbaceous than woody species. Simulation experiments indicate that BiChroM performs well with little to no bias and relatively little variance at a wide range of tree depths when trees have at least 500 taxa. Thus, BiChroM provides a first step toward a rigorous statistical framework for assessing the traits that facilitate polyploidy.

PREMISE OF THE STUDY: Whole-genome duplications (WGDs) can rapidly increase genome size in angiosperms. Yet their mean genome size is not correlated with ploidy. We compared three hypotheses to explain the constancy of genome size means across ploidies. The genome downsizing hypothesis suggests that genome size will decrease by a given percentage after a WGD. The genome size threshold hypothesis assumes that taxa with large genomes or large monoploid numbers will fail to undergo or survive WGDs. Finally, the genome downsizing and threshold hypothesis suggests that both genome downsizing and thresholds affect the relationship between genome size means and ploidy. METHODS: We performed nonparametric bootstrap simulations to compare observed angiosperm genome size means among species or genera against simulated genome sizes under the three different hypotheses. We evaluated the hypotheses using a decision theory approach and estimated the expected percentage of genome downsizing. KEY RESULTS: The threshold hypothesis improves the approximations between mean genome size and simulated genome size. At the species level, the genome downsizing with thresholds hypothesis best explains the genome size means with a 15% genome downsizing percentage. In the genus level simulations, the monoploid number threshold hypothesis best explains the data. CONCLUSIONS: Thresholdes of angiosperm genome sizes, and monoploid number is important for determining the genome size mean at the genus level.

Lemurs are often cited as an example of adaptive radiation, as more than 100 extant species have evolved and filled ecological niches on Madagascar. However, recent work suggests that lemurs lack a hallmark of other adaptive radiations: explosive speciation rates that decline over time. Thus, characterizing the tempo and mode of evolution in lemurs can reveal alternative ways that hyperdiverse clades arise over time, which might differ from traditional models. We explore lemur evolution using a phylogenomic dataset with broad taxonomic sampling that includes the lorisiforms of Asia and continental Africa. Our analyses reveal multiple bursts of diversification (without subsequent declines) that explain much of today’s lemur diversity. We also find higher rates of speciation in Madagascar’s lemurs compared to lorisiforms, and we demonstrate that the lemur clades with high diversification rates also have high rates of genomic introgression. This suggests that hybridization in these primates is not an evolutionary dead-end, but potential fuel for diversification. Considering the conservation crisis affecting strepsirrhine primates, with approximately 95% of species threatened with extinction, this study offers a perspective for explaining Madagascar’s primate diversity and reveals patterns of speciation, extinction, and gene flow that will help inform future conservation decisions. Here, the authors characterize the tempo and mode of lemur speciation with a phylogenomic dataset that also includes lorisiforms. They find that lemurs exhibited multiple bursts of diversification (without subsequent decline in diversification rate) with the highest diversification rates accompanied by high introgression rates.

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.