Continuous morphological variation correlated with genome size indicates frequent introgressive hybridization among Diphasiastrum species (Lycopodiaceae) in Central Europe

Does the evolution of micromorphology accompany chromosomal changes on dysploid and polyploid levels in the Barnardia japonica complex (Hyacinthaceae)?

BACKGROUND

Chromosome number and genome size changes via dysploidy and polyploidy accompany plant diversification and speciation. Such changes often impact also morphological characters. An excellent system to address the questions of how extensive and structured chromosomal changes within one species complex affect the phenotype is the monocot species complex of Barnardia japonica. This taxon contains two well established and distinct diploid cytotypes differing in base chromosome numbers (AA: x = 8, BB: x = 9) and their allopolyploid derivatives on several ploidy levels (from 3x to 6x). This extensive and structured genomic variation, however, is not mirrored by gross morphological differentiation.

RESULTS

The current study aims to analyze the correlations between the changes of chromosome numbers and genome sizes with palynological and leaf micromorphological characters in diploids and selected allopolyploids of the B. japonica complex. The chromosome numbers varied from 2n = 16 and 18 (2n = 25 with the presence of supernumerary B chromosomes), and from 2n = 26 to 51 in polyploids on four different ploidy levels (3x, 4x, 5x, and 6x). Despite additive chromosome numbers compared to diploid parental cytotypes, all polyploid cytotypes have experienced genome downsizing. Analyses of leaf micromorphological characters did not reveal any diagnostic traits that could be specifically assigned to individual cytotypes. The variation of pollen grain sizes correlated positively with ploidy levels.

CONCLUSIONS

This study clearly demonstrates that karyotype and genome size differentiation does not have to be correlated with morphological differentiation of cytotypes.

The integrated LIM-peptidase domain of the CSA1-CHS3/DAR4 paired immune receptor detects changes in DA1 peptidase inhibitors in Arabidopsis

White blister rust, caused by the oomycete Albugo candida, is a widespread disease of Brassica crops. The Brassica relative Arabidopsis thaliana uses the paired immune receptor complex CSA1-CHS3/DAR4 to resist Albugo infection. The CHS3/DAR4 sensor NLR, which functions together with its partner, the helper NLR CSA1, carries an integrated domain (ID) with homology to DA1 peptidases. Using domain swaps with several DA1 homologs, we show that the LIM-peptidase domain of the family member CHS3/DAR4 functions as an integrated decoy for the family member DAR3, which interacts with and inhibits the peptidase activities of the three closely related peptidases DA1, DAR1, and DAR2. Albugo infection rapidly lowers DAR3 levels and activates DA1 peptidase activity, thereby promoting endoreduplication of host tissues to support pathogen growth. We propose that the paired immune receptor CSA1-CHS3/DAR4 detects the actions of a putative Albugo effector that reduces DAR3 levels, resulting in defense activation.

Understanding the Taxonomic Complexes and Species Delimitation within Sambucus L. (Viburnaceae)

The genus Sambucus belongs to the family Viburnaceae, and has long been a debatable taxon regarding its systematics and taxonomic assignment. It is known for its morphological and genetic variations and thus the taxonomic delimitation remains uncertain. Phenotypic and genotypic variations within plant species causes difficulties in the detection of species boundaries. In the present review, we compiled a set of studies that assessed species discrimination within Sambucus genus by morphological and molecular markers as well as the taxonomic uncertainties in the re-circumscription of the segregated genera i.e., Viburnum L., Sambucus L., and Adoxa L., (syn. Sinadoxa C.Y. Wu, Z.L. Wu & R.F. Huang/Tetradoxa C.Y. Wu) from Caprifoliaceae and their family assignment. The data was obtained from published journal articles and various online databases. Morphological and molecular diagnostic characters were employed to distinguish Sambucus species. Our findings indicated that high intraspecific variations within narrow-ranged populations and their widespread counterparts contribute to its taxonomic complications. Additionally, intraspecific variations within Sambucus species leads to misidentifications and the misapplication of names, occasioning the publication of many putative synonyms and ambiguous names. Possible interspecific hybridizations experienced between Sambucus species increases complexity in character evolution. A morphological analysis showed that the endocarp seed morphological characters can reliably support the segregation of Sambucus taxa into discrete taxonomic entities. In molecular analysis, the NeighborNet (NN) phylogenetic split network revealed three distinct genera including Viburnum, Sambucus, and Adoxa, which clustered separately. The Maximum Likelihood (ML) analysis indicated that the Sambucus species formed a monophyletic group and clustered into two major clades, a small clade containing S. maderensis, S. peruviana, S. nigra, and S. canadensis, and a large clade encompassing the rest of the species with significantly supported clades (<52%). The preferred family assignment for Sambucus is Viburnaceae.

Measuring the Invisible: The Sequences Causal of Genome Size Differences in Eyebrights (Euphrasia) Revealed by k-mers

Genome size variation within plant taxa is due to presence/absence variation, which may affect low-copy sequences or genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation is challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies by design miss low-copy number sequences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole-genome sequencing data of diploid eyebrights (Euphrasia), a group of plants that have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further match high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We find genome size differences of up to 230Mbp, equivalent to more than 20% genome size variation. The largest contributions to these differences come from rDNA sequences, a 145-nt genomic satellite and a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class (copy number ≤ 10×) of up to 27 Mbp, possibly indicating differences in gene space between our samples. We demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without the use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats if they aim to characterise the full range of genomic variants. To allow future work with other taxonomic groups, we share our k-mer analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.

Club-mosses (Diphasiastrum, Lycopodiaceae) from the Far East - Introgression and possible cryptic speciation

Hybridization occurs often in the genus Diphasiastrum (Lycopodiaceae), which corroborates reports for the two other recognized lycophyte families, Isoëtaceae and Selaginellaceae. Here we investigate the case of D. alpinum and D. sitchense from the Russian Far East (Kamchatka). Their hybrid, D. × takedae, was morphologically recognizable in 16 out of 22 accessions showing molecular signatures of hybridization; the remaining accessions displayed the morphology of either D. alpinum (3) or D. sitchense (3). We sequenced markers for chloroplast microsatellites (cp, 175 accessions from Kamchatka) and for the two nuclear markers RPB and LFY (175 and 152 accessions). A selection of 42 accessions, including all hybrid accessions, was analysed via genotyping by sequencing (GBS). We found multiple, but apparently uniparental hybridization, clearly characterized by a deviating group of haplotypes for D. sitchense and all hybrids. All accessions showing molecular signatures of hybridization in nuclear markers revealed the parental haplotype of D. sitchense, however only the LFY marker differentiated between the parent species. GBS, including 69,819 quality-filtered single nucleotid polymorphisms, unambiguously identified the hybrids and revealed introgression to occur. Most of the hybrids were F₁, but three turned out to be backcrosses with D. alpinum (one) and with D. sitchense (two). These observations are in contrast to prior findings on three European species and their intermediates where all three hybrids turned out to be independent F₁ crosses without evidence of recent backcrossing. In this study, backcrossing was detected, which indicates a limited fertility of the hybrid taxon D. × takedae. A comparison of accessions of Kamchatkian D. alpinum with plants from Europe indicated possible cryptic speciation. Accessions from the Far East had (i) a lower DNA content (7.0 vs. 7.5 pg/2C), (ii) different prevailing cp haplotypes, and (iii) RPB genotypes, and (iv) a clearly different SNP pattern in GBS. Diphasiastrum sitchense and the similar D. nikoënse, for the latter additional accessions from Japan were investigated, appeared as forms of one diverse species, sharing genotypes in both nuclear markers, although chloroplast haplotypes and DNA content show slight variations.

Geographic Cline and Genetic Introgression Effects on Seed Morphology Variation and Germination Fitness in Two Closely Related Pine Species in Southeast Asia

There is still limited information on how genetic introgression impacts morphological variation and population fitness in long-lived conifer species. Two closely related pine species, Pinus kesiya Royle ex Gordon and Pinus yunnanensis Franch. are widely distributed over Southeast Asia and Yunnan province of China, with a large spatial scale of asymmetric genetic introgression and hybridization, and form a hybrid lineage, P. kesiya var. langbianensis, where their ranges overlap in southeast Yunnan. We compared seed trait variation and germination performance between hybrids and parental species and characterized environmental gradients to investigate the genetic and ecological evolutionary consequences of genetic introgression. We found that seed width (SW) differed significantly among the three pines, and all the seed traits were significantly negatively correlated with latitude and associated with the mean temperatures of the driest and wettest quarters. A higher germination fitness of hybrids was detected at a low temperature, indicating that they had better adaptability to temperature stress than their parental species during the germination process. Our results suggest that environmental factors shape seed phenotypic variation in the pine species and that genetic introgression significantly affects seed germination fitness. Therefore, assisting gene flow in natural forest populations might facilitate their adaptation to climate change.

The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights

BACKGROUND AND AIMS

Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species.

METHODS

We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples.

KEY RESULTS

We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small.

CONCLUSIONS

We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.

Sympatric genome size variation and hybridization of four oak species as determined by flow cytometry genome size variation and hybridization

The Quercus species serve as a powerful model for studying introgression in relation to species boundaries and adaptive processes. Coexistence of distant relatives, or lack of coexistence of closely relative oak species, introgression may play a role. In the current study, four closely related oak species were found in Zijinshan, China. We generated a comprehensive genome size (GS) database for 120 individuals of four species using flow cytometry-based approaches. We examined GS variability within and among the species and hybridization events among the four species. The mean GSs of Q. acutissima, Q. variabilis, Q. fabri, and Q. serrata var. brevipetiolata were estimated to be 1.87, 1.92, 1.97, and 1.97 pg, respectively. The intraspecific and interspecific variations of GS observed among the four oak species indicated adaptation to the environment. Hybridization occurred both within and between the sections. A hybrid offspring was produced from Q. fabri and Q. variabilis, which belonged to different sections. The GS evolutionary pattern for hybrid species was expansion. Hybridization between the sections may be affected by habitat disturbance. This study increases our understanding of the evolution of GS in Quercus and will help establish guidelines for the ecological protection of oak trees.

The rise of the Andes promoted rapid diversification in Neotropical Phlegmariurus (Lycopodiaceae)

Tropical mountains are disproportionately biodiverse relative to their surface area, but the processes underlying their exceptional diversity require further study. Here, we use comparative phylogenetic methods to examine the impact of the Andean orogeny on the diversification of Neotropical Phlegmariurus, a species-rich lycophyte clade. We generated a time-calibrated phylogeny of 105 species of Neotropical Phlegmariurus and estimated lineage diversification rates. We tested for correlations between lineage diversification rates and species range size, niche breadth, elevational range amplitude, and mean elevation of occurrence. A recently developed macroevolutionary model was used to incorporate geological data and test for an association between diversification rates and the Andean uplift. Diversification rates of Neotropical Phlegmariurus are negatively correlated with species range size and positively correlated with mean elevation of species occurrence. The rise of the Andes is strongly associated with increased rates of diversification in Neotropical Phlegmariurus during the last 10 Myr. Our study demonstrates the importance of mountain-building events and geographical isolation of alpine populations as drivers of rapid diversification, even in spore-dispersed plants. This work also highlights the usefulness of combined phylogenetic, geological and ecological datasets, and the promise of comparative environment-dependent diversification models in better understanding the evolutionary origins of biodiversity.

Genetic diversity and hybrid formation in Central European club-mosses (Diphasiastrum, Lycopodiaceae) - New insights from cp microsatellites, two nuclear markers and AFLP

In Europe, the genus Diphasiastrum (Lycopodiophyta) forms a reticulate network of six diploid taxa, including three parent species (D. alpinum, D. complanatum and D. tristachyum) and three hybrids (D. × issleri, D. × oellgaardii and D. × zeilleri). It was not clear if the hybrids arose once or repeatedly, if they have reproductive competence and if backcrossing occurs. We addressed these questions by analysing 209 accessions for chloroplast microsatellites (cp), two nuclear markers (introns of the RPB and LFY genes) and AFLP. For D. complanatum we show a sexual life cycle with alternation of generations: the gametophytic DNA amount is half of that of the sporophyte. With the exception of a single accession all hybrids display one of the two parental cp haplotypes; their frequencies do not differ significantly from a 1:1 ratio. Genotypes of nuclear markers are species-specific, displaying 2/4/1 (RPB) and 1/8/1 alleles (LFY) for the three parents mentioned above; all hybrids have one allele from each parent. All three hybrid taxa apparently represent independent F1 crosses. Hybridisation occurs bidirectional; no evidence for recent backcrossing was found. Asexual reproduction via agamospory is at least rare, since AFLP showed all hybrid plants to be different.

Crop-to-wild hybridization in cherries-Empirical evidence from Prunus fruticosa

Crop cultivation can lead to genetic swamping of indigenous species and thus pose a serious threat for biodiversity. The rare Eurasian tetraploid shrub Prunus fruticosa (ground cherry) is suspected of hybridizing with cultivated allochthonous tetraploid P. cerasus and autochthonous diploid P. avium. Three Prunus taxa (447 individuals of P. fruticosa, 43 of P. cerasus and 73 of P. avium) and their hybrids (198 individuals) were evaluated using analysis of absolute genome size/ploidy level and multivariate morphometrics. Flow cytometry revealed considerable differentiation in absolute genome size at the tetraploid level (average 2C of P. fruticosa = 1.30 pg, average 2C of P. cerasus = 1.42 pg, i.e., a 9.2% difference). The combination of methods used allowed us to ascertain the frequency of hybrids occurring under natural conditions in Central Europe. The morphological evaluation of leaves was based upon distance-based morphometrics supplemented by elliptic Fourier analysis. The results provided substantial evidence for ongoing hybridization (hybrids occurred in 39.5% of P. fruticosa populations). We detected homoploid introgressive hybridization with alien P. cerasus at the tetraploid level. We also found previously overlooked but frequent triploid hybrids resulting from heteroploid hybridization with indigenous P. avium, which, however, probably represent only the F1 generation. Although both hybrids differ in ploidy, they cannot be distinguished using morphometrics. Hybrids are frequent and may endanger wild populations of genuine P. fruticosa via direct niche competition or, alternatively or in addition, via introgression at the homoploid level (i.e., genetic swamping). The cultivation of cherries thus substantially threatens the existence of genuine P. fruticosa.

Heteroploid reticulate evolution and taxonomic status of an endemic species with bicentric geographical distribution

Reticulate evolution is considered to be among the main mechanisms of plant evolution, often leading to the establishment of new species. However, complex evolutionary scenarios result in a challenging definition of evolutionary and taxonomic units. In the present study, we aimed to examine the evolutionary origin and revise the species status of Campanula baumgartenii, a rare endemic species from the polyploid complex Campanula section Heterophylla. Morphometry, flow cytometric ploidy estimation, AFLPs, as well as chloroplast and nuclear DNA sequence markers were used to assess the morphological and genetic differentiation among C. baumgartenii, C. rotundifolia and other closely related taxa. Tetra- and hexaploid C. baumgartenii is morphologically and molecularly (AFLP) differentiated from sympatric C. rotundifolia. Contrasting signals from nuclear (ITS) and chloroplast (trnL-rpl32) markers suggest a hybrid origin of C. baumgartenii with C. rotundifolia and a taxon related to the alpine C. scheuchzeri as ancestors. Additionally, hexaploid C. baumgartenii currently hybridizes with co-occurring tetraploid C. rotundifolia resulting in pentaploid hybrids, for which C. baumgartenii serves as both seed and pollen donor. Based on the molecular and morphological differentiation, we propose to keep C. baumgartenii as a separate species. This study exemplifies that detailed population genetic studies can provide a solid basis for taxonomic delimitation within Campanula section Heterophylla as well as for sound identification of conservation targets.

Does hybridization with a widespread congener threaten the long-term persistence of the Eastern Alpine rare local endemic Knautia carinthiaca?

Interspecific hybridization, especially when regularly followed by backcrossing (i.e., introgressive hybridization), conveys a substantial risk for many endangered organisms. This is particularly true for narrow endemics occurring within distributional ranges of widespread congeners. An excellent example is provided by the plant genus Knautia (Caprifoliaceae): Locally endemic K. carinthiaca is reported from two isolated populations in southern Austria situated within an area predominantly occupied by widespread K. arvensis. While K. carinthiaca usually inhabits low-competition communities on rocky outcrops, K. arvensis occurs mainly in dry to mesic managed grasslands, yet both species can coexist in marginal environments and were suspected to hybridize. Flow cytometry revealed that diploid K. carinthiaca only occurs at its locus classicus, whereas the second locality is inhabited by the morphologically similar but tetraploid K. norica. In the, therefore, single population of K. carinthiaca, flow cytometry and AFLP fingerprinting showed signs of introgressive hybridization with diploid K. arvensis. Hybridization patterns were also reflected in intermediate habitat preferences and morphology of the hybrids. Environmental barriers to gene flow seem to prevent genetic erosion of K. carinthiaca individuals from the core ecological niches, restricting most introgressed individuals to peripheral habitats. Efficient conservation of K. carinthiaca will require strict protection of its habitat and ban on forest clear cuts in a buffer zone to prevent invasion of K. arvensis. We demonstrate the large potential of multidisciplinary approaches combining molecular, cytometric, and ecological tools for a reliable inventory and threat assessment of rare species.

Genome size as a key to evolutionary complex aquatic plants: polyploidy and hybridization in Callitriche (Plantaginaceae)

Despite their complex evolutionary histories, aquatic plants are highly underrepresented in contemporary biosystematic studies. Of them, the genus Callitriche is particularly interesting because of such evolutionary features as wide variation in chromosome numbers and pollination systems. However, taxonomic difficulties have prevented broader investigation of this genus. In this study we applied flow cytometry to Callitriche for the first time in order to gain an insight into evolutionary processes and genome size differentiation in the genus. Flow cytometry complemented by confirmation of chromosome counts was applied to an extensive dataset of 1077 Callitriche individuals from 495 localities in 11 European countries and the USA. Genome size was determined for 12 taxa. The results suggest that many important processes have interacted in the evolution of the genus, including polyploidization and hybridization. Incongruence between genome size and ploidy level, intraspecific variation in genome size, formation of autotriploid and hybridization between species with different pollination systems were also detected. Hybridization takes place particularly in the diploid-tetraploid complex C. cophocarpa-C. platycarpa, for which the triploid hybrids were frequently recorded in the area of co-occurrence of its parents. A hitherto unknown hybrid (probably C. hamulata × C. cophocarpa) with a unique chromosome number was discovered in the Czech Republic. However, hybridization occurs very rarely among most of the studied species. The main ecological preferences were also compared among the taxa collected. Although Callitriche taxa often grow in mixed populations, the ecological preferences of individual species are distinctly different in some cases. Anyway, flow cytometry is a very efficient method for taxonomic delimitation, determination and investigation of Callitriche species, and is even able to distinguish homoploid taxa and identify introduced species.