Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum

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.

Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum

Hybridization in bryophytes involves a fusion of gametes produced by haploid parental gametophytes of different species. The primary hybrid is thus the short-lived diploid sporophyte, which soon undergoes meiosis prior to the formation of large amounts of haploid spores. We compared morphology of gametophytes (branch leaves) and sporophytes (capsule inclination) from sympatric populations and allopatric populations of H. lutescens and H. sericeum. In addition, we used transcriptome data to select 85 nuclear SNP markers that were fixed for alternative alleles in the two species. The SNPs were used to estimate the degree of hybridization in diploid sporophytes. Our study shows that gametophytes from sympatric populations display intermediate morphology in a number of leaf characters, with exception for leaf sizes, which are markedly smaller than those in allopatric populations. None of the 100 sporophytes appeared to be primary hybrids, but 33 displayed admixing—heterozygotic expression of SNP markers or mismatch of occasional markers in homozygous condition—suggesting that extensive introgression takes place in the sympatric populations. Most sporophytes with intermediate capsule inclination, initially classed as putative hybrids, did not display admixture of nuclear SNP markers. Sixty-seven percent of admixed sporophytes have predominantly nuclear SNPs typical for H. lutescens. Our results suggest that interspecific hybridization and bidirectional introgression are relatively common in the studied sympatric populations, giving rise to viable recombinants, but not complete mixing of the parental genomes. Our study is one of the first detailed accounts of hybridization among pleurocarpous mosses, opening for future studies of gene transfer and introgression between bryophyte lineages and its role in local adaptation and long-term evolutionary diversification.

Evolutionary History of the Marchantia polymorpha Complex

The potential role of introgression in evolution has gained increased interest in recent years. Although some fascinating examples have been reported, more information is needed to generalize the importance of hybridization and introgression for adaptive divergence. As limited data exist on haploid dominant species, we analyzed genomes of three subspecies of the liverwort Marchantia polymorpha. We used available genomic data for subsp. ruderalis and carried out whole-genome (PacBio) sequencing for one individual each of subsp. montivagans and subsp. polymorpha as well as Illumina resequencing of additional genomes for all three subspecies. The three subspecies were compared against M. paleacea as outgroup. Our analyses revealed separation of the three taxa, but all three possible topologies were richly represented across the genomes, and the underlying divergence order less obvious. This uncertainty could be the result of the divergence of the three subspecies close in time, or that introgression has been frequent since divergence. In particular, we found that pseudo-chromosome 2 in subsp. montivagans was much more diverged than other parts of the genomes. This could either be explained by specific capture of chromosome 2 from an unknown related species through hybridization or by conservation of chromosome 2 despite intermittent or ongoing introgression affecting more permeable parts of the genomes. A higher degree of chromosomal rearrangements on pseudo-chromosome 2 support the second hypothesis. Species tree analyses recovered an overall topology where subsp. montivagans diverged first and subsp. ruderalis and subsp. polymorpha appeared as sister lineages. Each subspecies was associated with its own chloroplast and mitochondrial haplotype group. Our data suggest introgression but refute a previous hypothesis that subsp. ruderalis is a new stabilized hybrid between the other two subspecies.