Gene transfer by interspecific hybridization in bryophytes

Abstract

The role of hybridization in evolution has been debated for more than a century regarding bryophytes (mosses, liverworts, and hornworts) as well as most other organisms. Bryophytes have haplodiplontic life cycles with a dominant haploid generation. Hybridization in bryophytes involves fusion of gametes produced by haploid parental gametophytes of different species. The hybrid is thus the short-lived diploid sporophytes, which soon undergoes meiosis prior to forming a large amount of haploid recombinant spores. In this study, two moss species (Homalothecium lutescens and H. sericeum) and three subspecies of liverwort Marchantia polymorpha were investigated for evidence of gene transfer by hybridization.
Firstly, we compared the morphology of gametophytes and sporophytes from allopatric and sympatric populations of H. lutescens and H. sericeum. Secondly, we used species-specific SNP markers to estimate the degree of genetic mixing in three generations (i.e., haploid maternal gametophytes, diploid sporophytes, and haploid sporelings) in samples from sympatric populations of H. lutescens and H. sericeum. Thirdly, we assessed fitness traits in relation to the degree of genetic admixture in sporophytes of H. lutescens and H. sericeum, including non-admixed, mildly and strongly admixed genotypes. Finally, we investigated the genome-wide scale phylogenetic relationship between the three subspecies of M. polymorpha to test the hypothesis that subsp. ruderalis has originated as a homoploid hybrid species between subsp. polymorpha and subsp. montivagans.
Our study of Homalothecium shows that gametophytes from sympatric populations display intermediate morphology in a number of leaf characters, with the exception for leaf dimensions, which are strikingly smaller than those in allopatric populations. Most sporophytes with intermediate capsule inclination, initially classified as putative hybrids, did not display admixture of SNP markers. Many sporophytes appeared to be secondary hybrids by displaying asymmetrical admixture of SNP markers except five sporophytes, which were found to be primary hybrids. Admixture analyses using SNP markers identified 76 samples (17%) as mildly admixed and 17 samples (3.8%) as strongly admixed. Admixed samples represented all three generations and were found in all sympatric populations. Hybridization and introgression were bidirectional. Admixed sporophytes gave rise to viable recombinant spores and sporelings. Sporophytes with mildly admixed H. lutescens tended to show lower fitness, whereas sporophytes with mildly admixed H. sericeum showed signs of heterosis. Some strongly admixed sporophytes showed high spore counts, intermediate spore diameters and high spore germination rates.
Genomic analysis showed three distinct taxa within the M. polymorpha complex, coinciding with the three generally accepted subspecies. All three possible topologies were frequent across the genome but species tree analyses using M. paleacea as outgroup recovered an overall branching order where subsp. montivagans diverged first and subsp. ruderalis and subsp. polymorpha were placed as sister species. The high degree of inconsistent gene trees suggests frequent incomplete lineage sorting (ILS) and/or recent or intermittent introgression. Evidence for recent introgression was found in two samples of M. polymorpha. Remarkably, pseudo-chromosome 2 in subsp. montivagans differed by being 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 rearrangement in pseudochromosome 2 of subsp. montivagans provide some evidence for the latter explanation.
Our results show that gene transfer between lineages occurs in sympatric populations of both the Marchantia polymorpha complex and among the Homalothecium species. This supports the hypothesis that homoploid hybridization is more widespread among bryophytes than earlier assumed. Moreover, the population-level studies of sympatric populations of H. lutescens and H. sericeum demonstrate that they behave as true hybrid zones, where genetic material is transferred across species boundaries and secondarily backcrossed.
Presence of hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly subject of natural selection in the dominant haploid generation of the bryophyte life cycle, and contribute to local adaptation, survival and speciation.

Abstract (Swedish)

The role of hybridization in evolution has been debated for more than a century regarding bryophytes (mosses, liverworts, and hornworts) as well as most other organisms. Bryophytes have haplodiplontic life cycles with a dominant haploid generation. Hybridization in bryophytes involves fusion of gametes produced by haploid parental gametophytes of different species. The hybrid is thus the short-lived diploid sporophytes, which soon undergoes meiosis prior to forming a large amount of haploid recombinant spores. In this study, two moss species (Homalothecium lutescens and H. sericeum) and three subspecies of liverwort Marchantia polymorpha were investigated for evidence of gene transfer by hybridization.
Firstly, we compared the morphology of gametophytes and sporophytes from allopatric and sympatric populations of H. lutescens and H. sericeum. Secondly, we used species-specific SNP markers to estimate the degree of genetic mixing in three generations (i.e., haploid maternal gametophytes, diploid sporophytes, and haploid sporelings) in samples from sympatric populations of H. lutescens and H. sericeum. Thirdly, we assessed fitness traits in relation to the degree of genetic admixture in sporophytes of H. lutescens and H. sericeum, including non-admixed, mildly and strongly admixed genotypes. Finally, we investigated the genome-wide scale phylogenetic relationship between the three subspecies of M. polymorpha to test the hypothesis that subsp. ruderalis has originated as a homoploid hybrid species between subsp. polymorpha and subsp. montivagans.
Our study of Homalothecium shows that gametophytes from sympatric populations display intermediate morphology in a number of leaf characters, with the exception for leaf dimensions, which are strikingly smaller than those in allopatric populations. Most sporophytes with intermediate capsule inclination, initially classified as putative hybrids, did not display admixture of SNP markers. Many sporophytes appeared to be secondary hybrids by displaying asymmetrical admixture of SNP markers except five sporophytes, which were found to be primary hybrids. Admixture analyses using SNP markers identified 76 samples (17%) as mildly admixed and 17 samples (3.8%) as strongly admixed. Admixed samples represented all three generations and were found in all sympatric populations. Hybridization and introgression were bidirectional. Admixed sporophytes gave rise to viable recombinant spores and sporelings. Sporophytes with mildly admixed H. lutescens tended to show lower fitness, whereas sporophytes with mildly admixed H. sericeum showed signs of heterosis. Some strongly admixed sporophytes showed high spore counts, intermediate spore diameters and high spore germination rates.
Genomic analysis showed three distinct taxa within the M. polymorpha complex, coinciding with the three generally accepted subspecies. All three possible topologies were frequent across the genome but species tree analyses using M. paleacea as outgroup recovered an overall branching order where subsp. montivagans diverged first and subsp. ruderalis and subsp. polymorpha were placed as sister species. The high degree of inconsistent gene trees suggests frequent incomplete lineage sorting (ILS) and/or recent or intermittent introgression. Evidence for recent introgression was found in two samples of M. polymorpha. Remarkably, pseudo-chromosome 2 in subsp. montivagans differed by being 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 rearrangement in pseudochromosome 2 of subsp. montivagans provide some evidence for the latter explanation.
Our results show that gene transfer between lineages occurs in sympatric populations of both the Marchantia polymorpha complex and among the Homalothecium species. This supports the hypothesis that homoploid hybridization is more widespread among bryophytes than earlier assumed. Moreover, the population-level studies of sympatric populations of H. lutescens and H. sericeum demonstrate that they behave as true hybrid zones, where genetic material is transferred across species boundaries and secondarily backcrossed.
Presence of hybrid zones has strong evolutionary implications because genetic material transferred across species boundaries can be directly subject of natural selection in the dominant haploid generation of the bryophyte life cycle, and contribute to local adaptation, survival and speciation.

• author: Sawangproh, Weerachon
• supervisor: Nils Cronberg; Bengt Hansson; Ulf Lagercrantz
• opponent: Professor Hassel, Kristian, NTNU Trondheim, Department of Natural History, University Museum, Trondheim, Norway
• organization: Biodiversity
• publishing date: 2019-05-03
• type: Thesis
• publication status: published
• subject: Ecology
• keywords: homozygote, heterozygote, admixture, single nucleotide polymorphism, STRUCTURE, PCoA, hybrid index, inbreeding, outbreeding, hybrid depression, heterosis, phylogeny, purging selection, genetic purging, genotype, phenotype, sympatry, allopatry
• pages: 211 pages
• defense location: Lecture hall Blå hallen, the Ecology building, Sölvegatan 37, Lund
• defense date: 2019-05-03 13:00:00
• ISBN: 978-91-7895-020-1
• ISBN: 978-91-7895-021-8
• project: Hybridization as evolutionary driving force in bryophytes
• project: Fertilization syndromes in bryophytes
• language: English
• LU publication?: yes
• id: df204693-bfc0-489b-b662-5a8cde94171c
• date added to LUP: 2019-02-20 11:55:39
• date last changed: 2019-04-08 14:29:39