A population genetic model to infer allotetraploid speciation and long-term evolution applied to two yarrow species

Niche shifts and localized competitive dynamics influence the persistence and distribution of polyploids in the genus Achillea (Asteraceae)

BACKGROUND AND AIMS

Competition with sympatric diploid progenitor(s) hinders the persistence of polyploids. The hypothesis that polyploids escape from competition through niche shifts has been widely tested; however, niche escape is unlikely to completely avoid competition. Given species growing in less favourable environments probably have weaker competitive abilities, we hypothesize that polyploid populations tend to persist in areas where their progenitors have relatively low habitat suitability.

METHODS

This study investigated two sibling allopolyploid species, Achillea alpina and A. wilsoniana of the daisy family, which originated independently from the same two parental species. We explored the patterns of niche shifts between the polyploids and their progenitors by using several ecoinformatics analyses in environmental and geographical spaces, and performed ecological niche modelling to estimate the historical distribution of these species as well as the potential regions for persistence of allopolyploids.

KEY RESULTS

The niche shift patterns of the two polyploids were not completely consistent: A. alpina showed niche expansion, while A. wilsoniana exhibited a trend towards niche novelty. Their potential suitable areas were both more likely to overlap with regions where the habitat suitability values of their parental species became low.

CONCLUSIONS

The present results support our hypothesis that populations of polyploids tend to persist in areas that are less suitable for their diploid progenitors. Meanwhile, niche shifts may promote the success of polyploids. These findings contribute to our understanding of the ecological processes involved in the maintenance and persistence of polyploids.

Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae)

BACKGROUND

Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently.

RESULTS

We conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to "defense response". Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors.

CONCLUSION

Two independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids.

Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data

Polyploidy is common in the genus Salix. However, little is known about the origin, parentage and genomic composition of polyploid species because of a lack of suitable molecular markers and analysis tools. We established a phylogenomic framework including species of all described sections of Eurasian shrub willows. We analyzed the genomic composition of seven polyploid willow species in comparison to putative diploid parental species to draw conclusions on their origin and the effects of backcrossing and post-origin evolution. We applied recently developed programs like SNAPP, HyDe, and SNiPloid to establish a bioinformatic pipeline for unravelling the complexity of polyploid genomes. RAD sequencing revealed 23,393 loci and 320,010 high quality SNPs for the analysis of relationships of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix). Polyploid willow species appear to be predominantly of allopolyploid origin. More ancient allopolyploidization events were observed for two hexaploid and one octoploid species, while our data suggested a more recent allopolyploid origin for the included tetraploids and identified putative parental taxa. SNiPloid analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. Our RAD sequencing data demonstrate that willow genomes are shaped by ancient and recent reticulate evolution, polyploidization, and post-origin divergence of species.

Phylogenomic Relationships of Diploids and the Origins of Allotetraploids in Dactylorhiza (Orchidaceae)

Disentangling phylogenetic relationships proves challenging for groups that have evolved recently, especially if there is ongoing reticulation. Although they are in most cases immediately isolated from diploid relatives, sets of sibling allopolyploids often hybridize with each other, thereby increasing the complexity of an already challenging situation. Dactylorhiza (Orchidaceae: Orchidinae) is a genus much affected by allopolyploid speciation and reticulate phylogenetic relationships. Here, we use genetic variation at tens of thousands of genomic positions to unravel the convoluted evolutionary history of Dactylorhiza. We first investigate circumscription and relationships of diploid species in the genus using coalescent and maximum likelihood methods, and then group 16 allotetraploids by maximum affiliation to their putative parental diploids, implementing a method based on genotype likelihoods. The direction of hybrid crosses is inferred for each allotetraploid using information from maternally inherited plastid RADseq loci. Starting from age estimates of parental taxa, the relative ages of these allotetraploid entities are inferred by quantifying their genetic similarity to the diploids and numbers of private alleles compared with sibling allotetraploids. Whereas northwestern Europe is dominated by young allotetraploids of postglacial origins, comparatively older allotetraploids are distributed further south, where climatic conditions remained relatively stable during the Pleistocene glaciations. Our bioinformatics approach should prove effective for the study of other naturally occurring, nonmodel, polyploid plant complexes.

To be serrate or pinnate: diverse leaf forms of yarrows (Achillea) are linked to differential expression patterns of NAM genes

BACKGROUND AND AIMS

To understand the link between species diversity and phenotype developmental evolution is an important issue in evolutionary biology. Yarrows in the genus Achillea (Asteraceae) show a great diversity in leaf serrate or pinnate dissection patterns. In Arabidopsis thaliana, the development of leaf serration requires the activity of the transcription factor CUC2. Does this regulator also work for leaf dissections of the Asteraceae plants? If so, how do the conserved regulatory 'tools' work differently to produce diverse leaf forms?

METHODS

Seedling leaf morphology was observed, and morphogenesis of leaf serration or lobes was examined by scanning electron microscopy (SEM). NAM genes, orthologues of arabidopsis CUC2, were isolated from A. acuminata with serrate leaves and A. asiatica with three-pinnatisect leaves, respectively. By means of whole-mount in situ mRNA hybridization and two quantitative gene expression assays, the droplet digital PCR (ddPCR) and quantitative real-time PCR (qPCR), expression patterns of the NAM genes during leaf dissection development were checked in both species for comparison.

KEY RESULTS

For both species, the development of leaf dissection initiated when a leaf blade was about 300-400 µm long. In A. acuminata, in situ hybridization showed NAM expression signals at leaf margins where teeth are growing, or later on, in the sinuses of the teeth, whilst in A. asiatica, hybridization signals appear not only on leaf margins but further on the margins of leaf lobes. Both ddPCR and qPCR revealed a continuous decline of AacNAM expression from the early to the late developmental stages of a single leaf of A. acuminata, whereas a relatively long maintenance and fluctuation of AasNAM expression was seen in a leaf of A. asiatica.

CONCLUSIONS

Differential spatiotemporal patterns of NAM expression were found between the two yarrow species during development of leaf dissection. This study provides the first evidence for NAM activity in the development of leaf dissection of the Asteraceae plants, and demonstrates that leaf form diversity is correlated to the altered NAM expression dynamic.