[Show abstract][Hide abstract] ABSTRACT: Background
Plants colonized terrestrial environments approximately 480 million years ago and have contributed significantly to the diversification of life on Earth. Phylogenetic analyses position a subset of charophyte algae as the sister group to land plants, and distinguish two land plant groups that diverged around 450 million years ago – the bryophytes and the vascular plants. Relationships between liverworts, mosses hornworts and vascular plants have proven difficult to resolve, and as such it is not clear which bryophyte lineage is the sister group to all other land plants and which is the sister to vascular plants. The lack of comparative molecular studies in representatives of all three lineages exacerbates this uncertainty. Such comparisons can be made between mosses and liverworts because representative model organisms are well established in these two bryophyte lineages. To date, however, a model hornwort species has not been available.
Here we report the establishment of Anthoceros agrestis as a model hornwort species for laboratory experiments. Axenic culture conditions for maintenance and vegetative propagation have been determined, and treatments for the induction of sexual reproduction and sporophyte development have been established. In addition, protocols have been developed for the extraction of DNA and RNA that is of a quality suitable for molecular analyses. Analysis of haploid-derived genome sequence data of two A. agrestis isolates revealed single nucleotide polymorphisms at multiple loci, and thus these two strains are suitable starting material for classical genetic and mapping experiments.
Methods and resources have been developed to enable A. agrestis to be used as a model species for developmental, molecular, genomic, and genetic studies. This advance provides an unprecedented opportunity to investigate the biology of hornworts.
[Show abstract][Hide abstract] ABSTRACT: The masking hypothesis predicts that selection is more efficient in haploids than in diploids, because dominant alleles can
mask the deleterious effects of recessive alleles in diploids. However, gene expression breadth and noise can potentially
counteract the effect of masking on the rate at which genes evolve. Land plants are ideal to ask whether masking, expression
breadth, or expression noise dominate in their influence on the rate of molecular evolution, because they have a biphasic
life cycle in which the duration and complexity of the haploid and diploid phase varies among organisms. Here, we generate
and compile genome-wide gene expression, sequence divergence, and polymorphism data for Arabidopsis thaliana and for the moss Funaria hygrometrica to show that the evolutionary rates of haploid- and diploid-specific genes contradict the masking hypothesis. Haploid-specific
genes do not evolve more slowly than diploid-specific genes in either organism. Our data suggest that gene expression breadth
influence the evolutionary rate of phase-specific genes more strongly than masking. Our observations have implications for
the role of haploid life stages in the purging of deleterious mutations, as well as for the evolution of ploidy.
Preview · Article · May 2013 · Molecular Biology and Evolution
[Show abstract][Hide abstract] ABSTRACT: A taxonomic treatment based on field studies, examination of herbarium collections, and previously published molecular data is provided for the North American species of the Sphagnum subsecundum complex. Sphagnum platyphyllum, S. contortum, S. lescurii, and S. subsecundum are gametophytically haploid. Sphagnum missouricum and S. carolinianum are gametophytically allodiploid. A single allodiploid population of S. platyphyllum and a homoploid (haploid) hybrid between S. contortum and S. subscundum, previously documented genetically, are described and illustrated (but neither distinguished taxonomically). Epitypes are designated from (haploid) S. lescurii and (allodiploid) S. missouricum because the ploidal level of the original type material cannot be determined unambiguously. In North America, S. subsecundum is restricted to the eastern part of the continent, as western plants named this species are not conspecific. North American plants named S. inundatum are considered synonymous with either S. lescurii (when haploid) or S. missouricum (when diploid).
[Show abstract][Hide abstract] ABSTRACT: Abstract—The application of genetic tools for studying species delimitation and relationships in Sphagnum (peatmosses) has demonstrated that evolutionary patterns are complex and include homoploid hybridization and multiple taxa of allopolyploid origin. We investigated evolutionary relationships in the so-called S. fimbriatum complex and tested hypotheses of species delimitation derived from patterns of morphological variation, and determined the origin of one species with diploid gametophytes. Plastid DNA sequences resolve a single haplotype shared by one described species, S. concinnum, and a morphotype that we had hypothesized to be another species (referred to informally as S. “diskoense). All samples of the polyploid, S. tescorum, share an identical haplotype with most samples of S. girgensohnii. Sphagnum fimbriatum and S. girgensohnii share several plastid DNA haplotypes, and also share haplotypes with two other morphotypes that we had hypothesized to be distinct species (S. “obscurum and S. “ubertum). Fixed or nearly fixed heterozygosity at ten microsatellite loci show that S. tescorum is an allopolyploid. Genetic admixture analyses and computation of hybrid indices from microsatellite data, in combination with sequences from the plastid genome, support the hypothesis that S. fimbriatum and S. girgensohnii are progenitors of S. tescorum, with S. girgensohnii as the maternal parent. Data from 14 microsatellite loci demonstrate that S. concinnum, S. fimbriatum, S. girgensohnii, and S. tescorum are genetically distinct but the same data do not support separation of S. “diskoense, S. “obscurum, and S. “ubertum. Homoploid hybridization between S. fimbriatum and S. girgensohnii is strongly suggested by genetic data and phylogenetic analyses.
No preview · Article · Dec 2011 · Systematic Botany
[Show abstract][Hide abstract] ABSTRACT: Polyploidization is thought to result in instant sympatric speciation, but several cases of hybrid zones between one of the parental species and its polyploid derivative have been documented. Previous work showed that diploid Sphagnum lescurii is an allopolyploid derived from the haploids S. lescurii (maternal progenitor) and S. subsecundum (paternal progenitor). Here, we report the results from analyses of a population where allodiploid and haploid S. lescurii co-occur and produce sporophytes. We tested (i) whether haploids and diploids form hybrid triploid sporophytes; (ii) how hybrid and nonhybrid sporophytes compare in fitness; (iii) whether hybrid sporophytes form viable spores; (iv) the ploidy of any viable gametophyte offspring from hybrid sporophytes; (v) the relative viability of sporelings derived from hybrid and nonhybrid sporophytes; and (vi) if interploidal hybridization results in introgression between the allopolyploid and its haploid progenitor. We found that triploid hybrid sporophytes do occur and are larger than nonhybrid sporophytes, but exhibit very low germination percentages and produce sporelings that develop more slowly than those from nonhybrid sporophytes. All sporophytes attached to haploid gametophytes were triploid and were sired by diploid males, but all sporophytes attached to diploid gametophytes were tetraploid. This asymmetric pattern of interploidal hybridization is related to an absence of haploid male gametophytes in the population. Surprisingly, all sporelings from triploid sporophytes were triploid, yet were genetically variable, suggesting some form of aberrant meiosis that warrants further study. There was limited (but some) evidence of introgression between allodiploid and haploid S. lescurii.
No preview · Article · Jul 2011 · Molecular Ecology
[Show abstract][Hide abstract] ABSTRACT: Multiple paternity (polyandry) frequently occurs in flowering plants and animals and is assumed to have an important function in the evolution of reproductive traits. Polyandry in bryophytes may occur among multiple sporophytes of a female gametophyte; however, its occurrence and extent is unknown. In this study we investigate the occurrence and extent of multiple paternity, spatial genetic structure, and sporophytic inbreeding depression in natural populations of a dioicous bryophyte species, Sphagnum lescurii, using microsatellite markers. Multiple paternity is prevalent among sporophytes of a female gametophyte and male genotypes exhibit significant skew in paternity. Despite significant spatial genetic structure in the population, suggesting frequent inbreeding, the number of inbred and outbred sporophytes was balanced, resulting in an average fixation coefficient and population level selfing rate of zero. In line with the prediction of sporophytic inbreeding depression sporophyte size was significantly correlated with the level of heterozygosity. Furthermore, female gametophytes preferentially supported sporophytes with higher heterozygosity. These results indicate that polyandry provides the opportunity for postfertilization selection in bryophytes having short fertilization distances and spatially structured populations facilitating inbreeding. Preferential maternal support of the more heterozygous sporophytes suggests active inbreeding avoidance that may have significant implications for mating system evolution in bryophytes.
[Show abstract][Hide abstract] ABSTRACT: This paper documents the occurrence of allotriploidy (having three differentiated genomes) in gametophytes of two Southern Hemisphere Sphagnum species (S. australe, S. falcatulum). The pattern of microsatellite alleles indicates that both species are composed of a complex of allodiploid and allotriploid gametophytes, with the latter resulting from two allopolyploidization events. No haploid (n = x) gametophytes were found for either species. The ploidal levels suggested by the pattern of microsatellite alleles were confirmed by flow cytometry and Feulgen DNA image densitometry. For both S. australe and S. falcatulum, the respective allodiploid plants (or their ancestors) are one of the parent species of the allotriploid plants. This is the first report of triploidy in Sphagnum gametophytes occurring in nature and also the first report of the presence of three differentiated genomes in any bryophyte. It is also the first report of intersectional allopolyploidy in Sphagnum, with S. australe appearing to have parental species from Sphagnum sections Rigida and Sphagnum, and S. falcatulum having parental species from Sphagnum sections Cuspidata and Subsecunda. In both species, the allotriploid cytotypes were the most prevalent cytotype on the South Island of New Zealand. The pattern of microsatellite alleles shows the presence of two genetically distinct populations of allodiploid S. australe, possibly indicating multiple origins of polyploidy for that allodiploid cytotype. Morphological evidence is also highly indicative of recurrent polyploidy in the allotriploid cytotype of S. falcatulum. Allopolyploidy has clearly played a major evolutionary role in these two Southern Hemisphere taxa. This study, in conjunction with other recent research, indicates that allopolyploidy is a common, if not the predominant, form of polyploidy in Sphagnum.
No preview · Article · May 2009 · Molecular Ecology
[Show abstract][Hide abstract] ABSTRACT: Several lines of evidence suggest that recent long-distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi-Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (IM and MIGRATE) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F(ST) = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long-range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000-289,000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi-Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.
Full-text · Article · Jan 2009 · Molecular Ecology
[Show abstract][Hide abstract] ABSTRACT: Allopolyploid speciation is likely the predominant mode of sympatric speciation in plants. The Sphagnum subsecundum complex includes six species in North America. Three have haploid gametophytes, and three are thought to have diploid gametophytes. Microsatellite analyses indicated that some plants of S. inundatum and S. lescurii are heterozygous at most loci, but others have only one allele at each locus. Flow cytometry and Feulgen staining showed that heterozygous plants have twice the genome size as plants with one allele per locus; thus, microsatellite patterns can be used to survey the distribution and abundance of haploid and diploid gametophytes. Microsatellite analyses also revealed that S. carolinianum is consistently diploid, but S. lescurii and S. inundatum include both haploid and diploid populations. The frequency of diploid plants in S. lescurii increases with latitude. In an analysis of one population of S. lescurii, both cytotypes co-occurred but were genetically differentiated with no evidence of interbreeding. The degree of genetic differentiation showed that the diploids were not derived from simple genome duplication of the local haploids. Heterozygosity appears to be fixed or nearly so in diploids, strongly suggesting that although morphologically indistinguishable from the haploids, they are derived by allopolyploidy.
Full-text · Article · Dec 2008 · American Journal of Botany
[Show abstract][Hide abstract] ABSTRACT: Allopolyploidy is probably the most extensively studied mode of plant speciation and allopolyploid species appear to be common in the mosses (Bryophyta). The Sphagnum subsecundum complex includes species known to be gametophytically haploid or diploid, and it has been proposed that the diploids (i.e., with tetraploid sporophytes) are allopolyploids. Nucleotide sequence and microsatellite variation among haploids and diploids from Newfoundland and Scandinavia indicate that (1) the diploids exhibit fixed or nearly fixed heterozygosity at the majority of loci sampled, and are clearly allopolyploids, (2) diploids originated independently in North America and Europe, (3) the European diploids appear to have the haploid species, S. subsecundum, as the maternal parent based on shared chloroplast DNA haplotypes, (4) the North American diploids do not have the chloroplast DNA of any sampled haploid, (5) both North American and European diploids share nucleotide and microsatellite similarities with S. subsecundum, (6) the diploids harbor more nucleotide and microsatellite diversity than the haploids, and (7) diploids exhibit higher levels of linkage disequilibrium among microsatellite loci. An experiment demonstrates significant artifactual recombination between interspecific DNAs coamplified by PCR, which may be a complicating factor in the interpretation of sequence-based analyses of allopolyploids.
Full-text · Article · Oct 2008 · Molecular Phylogenetics and Evolution
[Show abstract][Hide abstract] ABSTRACT: Eight microsatellite loci from the aquatic moss Platyhypnidium riparioides were identified using the method of microsatellite-enriched libraries. Polymorphism was assessed in a sample of four populations of 20 individuals each from four streams of the Meuse hydrographic basin in southern Belgium. The markers amplified three to seven alleles per locus. Comparison of observed and expected heterozygosities as well as F-statistics (F(ST) = 0.62) reveals a significant genetic differentiation among populations. These markers will be useful for further investigation of population genetic structure and diversity at different nested spatial scales.
[Show abstract][Hide abstract] ABSTRACT: Thanks to its attractive phylogenetic position and molecular genetic attributes the model moss, Physcomitrella patens, has become a powerful tool for developmental and molecular genetic research during the last decade. Although many of the advantageous properties of the bryophyte system have been used in studies on development and cellular function, several peculiar characteristics have not received much attention so far. In particular, evolutionary genomics and comparative developmental genomics of mosses are still in their infancy and are waiting to be exploited. Here we report genome sequencing of Funaria hygrometrica, a relative of the model moss P. patens, using new generation sequencing technology (454, Illumina and Pacific Bioscience). Our current assembly consists of 10 000 scaffolds with an N50 scaffold length of 73kb (assembled using 80x Illumina and 3x 454 data) which is estimated to cover appr. 92% of the F. hygrometrica genome. We are currently working on improving this assembly by adding 4x of PacBio data and Illumina jumping libraries (3kb and 5kb) to aid scaffolding and gap filling. In a parallel effort we are re-sequencing multiple Funaria, Physcomitrium and Physcomitrella strains to explore the genomic mechanisms of rapid sporophyte evolution in the Funariid mosses. Funaria and Physcomitrella represent contrasting morphological and developmental complexities within the group of Funariid mosses and thus provide an ideal model system for comparative studies. Availability of the F. hygrometrica genome will open up new fields in non-vascular plant research by providing novel insights into the comparative genomics, developmental biology and evolutionary genomics of the Funariid mosses.