Bromeliaceae subfamilies show divergent trends of genome size evolution

Genome size variation and polyploidy prevalence in the genus Eragrostis are associated with the global dispersal in arid area

BACKGROUND

Biologists have long debated the drivers of the genome size evolution and variation ever since Darwin. Assumptions for the adaptive or maladaptive consequences of the associations between genome sizes and environmental factors have been proposed, but the significance of these hypotheses remains controversial. Eragrostis is a large genus in the grass family and is often used as crop or forage during the dry seasons. The wide range and complex ploidy levels make Eragrostis an excellent model for investigating how the genome size variation and evolution is associated with environmental factors and how these changes can ben interpreted.

METHODS

We reconstructed the Eragrostis phylogeny and estimated genome sizes through flow cytometric analyses. Phylogenetic comparative analyses were performed to explore how genome size variation and evolution is related to their climatic niches and geographical ranges. The genome size evolution and environmental factors were examined using different models to study the phylogenetic signal, mode and tempo throughout evolutionary history.

RESULTS

Our results support the monophyly of Eragrostis. The genome sizes in Eragrostis ranged from ~0.66 pg to ~3.80 pg. We found that a moderate phylogenetic conservatism existed in terms of the genome sizes but was absent from environmental factors. In addition, phylogeny-based associations revealed close correlations between genome sizes and precipitation-related variables, indicating that the genome size variation mainly caused by polyploidization may have evolved as an adaptation to various environments in the genus Eragrostis.

CONCLUSION

This is the first study to take a global perspective on the genome size variation and evolution in the genus Eragrostis. Our results suggest that the adaptation and conservatism are manifested in the genome size variation, allowing the arid species of Eragrostis to spread the xeric area throughout the world.

Altitudinal Patterns in Adaptive Evolution of Genome Size and Inter-Genome Hybridization Between Three Elymus Species From the Qinghai–Tibetan Plateau

Genome size variation and hybridization occur frequently within or between plant species under diverse environmental conditions, which enrich species diversification and drive the evolutionary process. Elymus L. is the largest genus in Triticeae with five recognized basic genomes (St, H, P, W, and Y). However, the data on population cytogenetics of Elymus species are sparse, especially whether genome hybridization and chromosomal structure can be affected by altitude are still unknown. In order to explore the relationship between genome sizes, we studied interspecific hybridization and altitude of Elymus species at population genetic and cytological levels. Twenty-seven populations at nine different altitudes (2,800–4,300 m) of three Elymus species, namely, hexaploid E. nutans (StHY, 2n = 6x = 42), tetraploid E. burchan-buddae (StY, 2n = 4x = 28), and E. sibiricus (StH, 2n = 4x = 28), were sampled from the Qinghai–Tibetan Plateau (QTP) to estimate whether intraspecific variation could affect the genomic relationships by genomic in situ hybridization (GISH), and quantify the genome size of Elymus among different altitude ecological groups by flow cytometry. The genome size of E. nutans, E. burchan-buddae, and E. sibiricus varied from 12.38 to 22.33, 8.81 to 18.93, and 11.46 to 20.96 pg/2C with the averages of 19.59, 12.39, and 16.85 pg/2C, respectively. The curve regression analysis revealed a strong correlation between altitude and nuclear DNA content in three Elymus species. In addition, the chromosomes of the St and Y genomes demonstrated higher polymorphism than that of the H genome. Larger genome size variations occurred in the mid-altitude populations (3,900–4,300 m) compared with other-altitude populations, suggesting a notable altitudinal pattern in genome size variation, which shaped genome evolution by altitude. This result supports our former hypothesis that genetic richness center at medium altitude is useful and valuable for species adaptation to highland environmental conditions, germplasm utilization, and conservation.

Pomological Traits and Genome Size of Prunus armeniaca L. Considering to Geographical Origin

Apricot (Prunus armeniaca L.) is an important fruit crop and member of the Prunus genus of the Rosaceae family that is planted in many temperate regions worldwide. The quality of fruit is assessed by many pomological parameters which can serve as a decisive factor in apricot breeding, because the introduction of new cultivars is required. These parameters can differ with climate conditions, geographical location or geographic ecological origin. Similarly, another biological characteristic can be measured depending on these terms. The present study was conducted with the aim of estimating pomological traits together with the nuclear DNA content of 35 apricot cultivars with different geographical origins. Only CV values lower than 5% were considered in flow cytometry analysis. All analyzed cultivars were diploid and the genome size value ranged from 0.587 to 0.644 pg/2C, where Turkish apricots reached the highest value (on average 0.628 pg/2C) followed by the European group (on average 0.625 pg/2C). A Spearman-rank correlation was used and the different correlation was found for specific geographical groups of apricot cultivars. The genome size values of apricots and related botanical species P. mume, P. sibirica and P. ansu showed to be very similar values.

Incongruent phylogenies and their implications for the study of diversification, taxonomy, and genome size evolution of Rhododendron

PREMISE

Classification of taxa depends on the quality of inferred phylogenies. Rhododendron, a highly species-rich genus (>1156 species) of woody plants, has a highly debated infrageneric classification, due to its huge diversity, homoplasy in key characters, and incongruence among data sets. We provide a broad coverage of representative species to resolve Rhododendron infrageneric phylogeny and highlight the areas of incongruence. We further investigate the effect of polyploidy and genome size evolution on diversification of Rhododendron.

METHODS

We generated two plastid and two nuclear loci for 260 Rhododendron species. We analyzed the loci separately as well as concatenated, utilizing both likelihood and Bayesian methods. We tested incongruence both among the data sets and with previous studies. We estimated genome sizes for 125 species through flow cytometry.

RESULTS

Our results suggest stronger support for larger subgenera; however, the smaller subgenera pose several problems; for example, R. tomentosum (former genus Ledum) occupies incongruent positions based on different DNA regions. The main shift to higher diversification in the genus occurs in the Himalayan/Southeast Asian clade of R. subg. Hymenanthes. We found that polyploidy occurs in almost all subgenera but most frequently within R. subg. Rhododendron sections Rhododendron and Schistanthe.

CONCLUSIONS

We endorse the recognition of five major clades at the subgeneric level, but a number of species cannot be confidently assigned to these clades due to incongruency. With regard to genome size evolution, results support previous reports that genome sizes of tropical plants are lower than those of colder and temperate regions and that genome downsizing promotes diversification.

Genome size evolution is associated with climate seasonality and glucosinolates, but not life history, soil nutrients or range size, across a clade of mustards

BACKGROUND AND AIMS

We investigate patterns of evolution of genome size across a morphologically and ecologically diverse clade of Brassicaceae, in relation to ecological and life history traits. While numerous hypotheses have been put forward regarding autecological and environmental factors that could favour small vs. large genomes, a challenge in understanding genome size evolution in plants is that many hypothesized selective agents are intercorrelated.

METHODS

We contribute genome size estimates for 47 species of Streptanthus Nutt. and close relatives, and take advantage of many data collections for this group to assemble data on climate, life history, soil affinity and composition, geographic range and plant secondary chemistry to identify simultaneous correlates of variation in genome size in an evolutionary framework. We assess models of evolution across clades and use phylogenetically informed analyses as well as model selection and information criteria approaches to identify variables that can best explain genome size variation in this clade.

KEY RESULTS

We find differences in genome size and heterogeneity in its rate of evolution across subclades of Streptanthus and close relatives. We show that clade-wide genome size is positively associated with climate seasonality and glucosinolate compounds. Model selection and information criteria approaches identify a best model that includes temperature seasonality and fraction of aliphatic glucosinolates, suggesting a possible role for genome size in climatic adaptation or a role for biotic interactions in shaping the evolution of genome size. We find no evidence supporting hypotheses of life history, range size or soil nutrients as forces shaping genome size in this system.

CONCLUSIONS

Our findings suggest climate seasonality and biotic interactions as potential forces shaping the evolution of genome size and highlight the importance of evaluating multiple factors in the context of phylogeny to understand the effect of possible selective agents on genome size.

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.

On the Selection and Analysis of Clades in Comparative Evolutionary Studies

Researchers commonly present results of comparative studies of taxonomic groups. In this review, we criticize the focus on named clades, usually, comparably ranked groups such as families or orders, for comparative evolutionary analyses and question the general practice of using clades as units of analysis. The practice of analyzing sets of named groups persists despite widespread appreciation that the groups we have chosen to name are based on subjective human concerns rather than objective properties of nature. We demonstrate an effect of clade selection on results in one study and present some potential alternatives to selecting named clades for analysis that are relatively objective in clade choice. However, we note that these alternatives are only partial solutions for clade-based studies. The practice of analyzing named clades obviously is biased and problematic, but its issues portend broader problems with the general approach of employing clades as units of analysis. Most clade-based studies do not account for the nonindependence of clades, and the biological insight gained from demonstrating some pattern among a particular arbitrary sample of groups is arguable. [Clades; comparative biology; taxonomic groups.].

Early Diverging and Core Bromelioideae (Bromeliaceae) Reveal Contrasting Patterns of Genome Size Evolution and Polyploidy

The subfamily Bromelioideae is one of the most diverse groups among the neotropical Bromeliaceae. Previously, key innovations have been identified which account for the extraordinary radiation and species richness of this subfamily, especially in the so-called core Bromelioideae. However, in order to extend our understanding of the evolutionary mechanisms, the genomic mechanisms (e.g. polyploidy, dysploidy) that potentially underlie this accelerated speciation also need to be tested. Here, using PI and DAPI staining and flow cytometry we estimated genome size and GC content of 231 plants covering 30 genera and 165 species and combined it with published data. The evolutionary and ecological significance of all three genomic characters was tested within a previously generated dated phylogenetic framework using ancestral state reconstructions, comparative phylogenetic methods, and multiple regressions with climatic variables. The absolute genome size (2C) of Bromelioideae varied between 0.59 and 4.11 pg, and the GC content ranged between 36.73 and 41.43%. The monoploid genome sizes (Cx) differed significantly between core and early diverging lineages. The occurrence of dysploidy and polyploidy was, with few exceptions, limited to the phylogenetically isolated early diverging tank-less lineages. For Cx and GC content Ornstein-Uhlenbeck models outperformed the Brownian motion models suggesting adaptive potential linked to the temperature conditions. 2C-values revealed different rates of evolution in core and early diverging lineages also related to climatic conditions. Our results suggest that polyploidy is not associated with higher net diversification and fast radiation in core bromelioids. On the other hand, although coupled with higher extinction rates, dysploidy, polyploidy, and resulting genomic reorganizations might have played a role in the survival of the early diverging bromelioids in hot and arid environments.