Biology subjects

McDaniel, S. F.

Publications and source records attributed to McDaniel, S. F..

9 recordsLinked to original sources

bioRxiv2026

Moss Transplants in the Tundra Reveal Host-Specific Microbiomes and Nitrogen Fixation Responses

In tundra ecosystems, moss-associated microbes are a major source of new nitrogen, yet the relative contributions of environment, host identity, and microbiome composition to variation in nitrogen-fixation rates are difficult to disentangle. To test how environmental change alters moss microbiomes and nitrogen-fixation rates, we used a one-year reciprocal transplant experiment between two Alaskan tundra sites that differ by 5{degrees}C in mean annual temperature. Intact moss cores containing one of three moss species, Hylocomium splendens, Aulacomnium turgidum, and Pleurozium schreberi, were transplanted between sites or returned to their home site. After one year, we quantified nitrogen-fixation rates using 15N incubation and characterized bacterial communities using 16S rRNA gene amplicon sequencing. H. splendens showed consistently low nitrogen-fixation rates with little transplant response, whereas P. schreberi and A. turgidum home and transplant tundra cores generally exhibited higher rates at the cooler, more northern site regardless of origin. In contrast, bacterial community structure changed little following transplantation, with composition driven primarily by moss species. Only in cyanobacteria and some heterotrophic bacterial lineages did we find subtle ASV-level changes. The absence of an association between microbial composition and nitrogen fixation, together with the heterogeneity among moss species, suggests that over short timescales, host physiology and microenvironment play a larger role in the variation of nitrogen-fixation rates than community turnover. The fact that short-term shifts in moss-associated nitrogen-fixation rate are driven primarily by host species identity, rather than microbiome restructuring, has important implications for near-term predictions of nitrogen inputs under Arctic climate change.

microbiology↗

bioRxiv2024

Testing for the genomic footprint of conflict between life stages in an angiosperm and a moss species

The maintenance of genetic variation by balancing selection is of considerable interest to evolutionary biologists. An important but understudied potential driver of balancing selection is antagonistic pleiotropy between diploid and haploid stages of the plant life cycle. Despite sharing a common genome, sporophytes (2n) and gametophytes (n) may undergo differential or even opposing selection. Theoretical work suggests the antagonistic pleiotropy between life stages can generate balancing selection and maintain genetic variation. Despite the potential for far-reaching consequences of gametophytic selection, empirical tests of its pleiotropic effects (neutral, synergistic, or antagonistic) on sporophytes are generally lacking. Here, we examined the population genomic signals of selection across life stages in the angiosperm Rumex hastatulus and the moss Ceratodon purpureus. We compared gene expression among life stages and between sexes, combined with neutral diversity statistics and the analysis of the distribution of fitness effects. In contrast to what would be predicted under balancing selection due to antagonistic pleiotropy, we found that unbiased genes between life stages were under stronger purifying selection, likely explained by a predominance of synergistic pleiotropy between life stages and strong purifying selection on broadly expressed genes. In addition, we found that 30% of candidate genes under balancing selection in R. hastatulus were located within inversion polymorphisms. Our findings provide novel insights into the genome-wide characteristics and consequences of plant gametophytic selection. SignificanceThe genome-wide importance of balancing selection has been a key question in evolutionary biology. Despite theoretical support for the potential of balancing selection generated by antagonistic pleiotropy between plant life stages, to our knowledge no empirical studies have systematically investigated this on a genome-wide scale. Our results revealed genome-wide patterns more consistent with synergistic pleiotropy, with gametophyte-biased genes more likely to be under relaxed purifying selection in both the angiosperm and moss species we investigated. In addition, our study suggests gene expression level and breadth has a greater effect on selection efficacy than differences between ploidy levels in different life stages.

evolutionary biology↗

bioRxiv2023

Establishing CRISPR-Cas9 in the sexually dimorphic moss, Ceratodon purpureus.

The development of CRISPR technologies provides a powerful tool for understanding the evolution and functionality of essential biological processes. Here we demonstrate successful CRISPR-Cas9 genome editing in the dioecious moss species, Ceratodon purpureus. Using an existing selection system from the distantly related hermaphroditic moss, Physcomitrium patens, we generated knock-outs of the APT reporter gene by employing CRISPR targeted mutagenesis under expression of native U6 snRNA promoters. Next, we used the native homology-directed repair (HDR) pathway, combined with CRISPR-Cas9, to knock-in two reporter genes under expression of an endogenous RPS5A promoter in a newly developed landing site in C. purpureus. Our results show that the molecular tools developed in P. patens can be extended to other mosses across this ecologically important and developmentally variable group. These findings pave the way for precise and powerful experiments aimed at identifying the genetic basis of key functional variation within the bryophytes and between the bryophytes and other land plants. Significance StatementWe have developed CRISPR-Cas9 genome editing tools and protocols for the sexually dimorphic moss, Ceratodon purpureus to generate gene knock-outs and knock-ins within targeted loci. This work facilitates future functional genomic experiments in this fast growing, haploid, dioecious system and suggests these tools will function across much of moss diversity.

molecular biology↗

bioRxiv2021

Novel insights into joint estimations of demography, mutation rate, and selection using UV sex chromosomes

A central goal in evolutionary genomics is to understand the processes that shape genetic variation in natural populations. In anisogamous species, these processes may generate asymmetries between genes transmitted through sperm or eggs. The unique inheritance of sex chromosomes facilitates studying such asymmetries, but in many systems sex-biased mutation, demography, and selection are confounded with suppressed recombination in only one sex (the W in females, or the Y in males). However, in a UV sex-determination system, both sex chromosomes are sex-specific and experience suppressed recombination. Here we built a spatially-structured simulation to examine the effects of population density and sex-ratio on female and male effective population size in haploids and compare the results to polymorphism data from whole-genome resequencing of the moss Ceratodon purpureus. In the parameter space we simulated, males nearly always had a lower effective population size than females. Using the C. purpureus resequencing data, we found the U and V have lower nucleotide diversity than the autosomal mean, and the V is much lower than the U, however, we found no parameter set in the model that explained both the U/V and U/autosome ratios we observed. We next used standard molecular evolutionary analyses to test for sex-biased mutation and selection. We found that males had a higher mutation rate but that natural selection shapes variation on the UV sex chromosomes. All together the moss system highlights how anisogamy alone can exert a profound influence on genome-wide patterns of molecular evolution.

evolutionary biology↗

bioRxiv2020

Microarthropod contributions to fitness variation in the common moss Ceratodon purpureus

The evolution of mutualism depends critically upon genetic variation in the fitness benefit to both partners. Estimates of these quantities are rare, however, because genetic variation for the interaction may be absent, aspects of the interaction may not be amenable to experimental manipulation, or the benefits to one partner may be unknown. In vitro experiments show that female mosses produce odors which attract sperm-dispersing microarthropods, but the fitness consequences of this interaction for either partner are unknown. Here we established experimental mesocosms to test for a commensal effect of sperm-dispersing microarthropods on moss reproduction. We found that of moss grown with microarthropods showed increased moss reproductive rates by five times, relative to control mesocosms, but remarkably also increased the number of reproducing genotypes, and changed the rank-order of fitness for both male and female genotypes. These results provide an estimate of the fitness benefit for mosses in the presence of microarthropods, and highlight the potential for biotic dispersal agents to alter fitness among moss genotypes in this relationship.

plant biology↗

bioRxiv2020

A target enrichment probe set for resolving the flagellate plant tree of life

Premise of the studyNew sequencing technologies enable the possibility of generating large-scale molecular datasets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and gymnosperms. Methods and ResultsWe leveraged existing transcriptome and genome sequence data to design a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding flanking regions across flagellate plant lineages. We describe the performance of target enrichment using the probe set across flagellate plants and demonstrate the potential of the data to resolve relationships among both ancient and closely related taxa. ConclusionsA target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate plants.

evolutionary biology↗

bioRxiv2020

Area from image analyses accurately estimates dry-weight biomass of juvenile moss tissue

O_LIMosses have long served as models for studying many areas of plant biology. Investigators have used two-dimensional measurements of juvenile growth from photographs as a surrogate for dry-weight biomass. The relationship between area and biomass, however, has not been critically evaluated. C_LIO_LIHere we grew axenic tissue cultures of ten Ceratodon purpureus isolates to study the relationship between these parameters. We measured area and biomass on replicate cultures with two distinct starting inoculum sizes each week for three weeks and examined the correlation between area and biomass as well as the influence of variation in inoculum size on both parameters. C_LIO_LIWe found a strong correlation between area and biomass after two weeks of growth. Furthermore, we found inoculum size affected biomass during the first week of growth but not subsequent weeks and inoculum size had no detectible effect on area. C_LIO_LIThese analyses provide experimental confirmation that area is a suitable proxy for biomass and provide clear guidelines for when inoculum size variation may affect downstream growth estimates. C_LI

plant biology↗

bioRxiv2017

Peripatric speciation associated with genome expansion and female-biased sex ratios in the moss genus Ceratodon

PREMISE OF THE STUDYA period of allopatry is widely believed to be essential for the evolution of reproductive isolation. However, strict allopatry may be difficult to achieve in some cosmopolitan, spore-dispersed groups, like mosses. Here we examine the genetic and genome size diversity in Mediterranean populations of the moss Ceratodon purpureus s.l. to evaluate the role of allopatry and ploidy change in population divergence.\n\nMETHODSWe sampled populations of the genus Ceratodon from mountainous areas and lowlands of the Mediterranean region, and from western and central Europe. We performed phylogenetic and coalescent analyses on sequences from five nuclear introns and a chloroplast locus to reconstruct their evolutionary history. We also estimated the genome size using flow cytometry, employing propidium iodide, and determined their sex using a sex-linked PCR marker.\n\nKEY RESULTSTwo well differentiated clades were resolved, discriminating two homogeneous groups: the widespread C. purpureus and a local group mostly restricted to the mountains in southern Spain. The latter also possessed a genome size 25% larger than the widespread C. purpureus, and the samples of this group consist entirely of females. We also found hybrids, and some of them had a genome size equivalent to the sum of the C. purpureus and Spanish genome, suggesting that they arose by allopolyploidy.\n\nCONCLUSIONSThese data suggest that a new species of Ceratodon arose via peripatric speciation, potentially involving a genome size change and a strong female-biased sex ratio. The new species has hybridized in the past with C. purpureus.

molecular biology↗

bioRxiv2017

Novel bacterial lineages associated with boreal moss species

Mosses are critical components of boreal ecosystems where they typically account for a large proportion of net primary productivity and harbor diverse bacterial communities that can be the major source of biologically-fixed nitrogen in these ecosystems. Despite their ecological importance, we have limited understanding of how microbial communities vary across boreal moss species and the extent to which local environmental conditions may influence the composition of these bacterial communities. We used marker gene sequencing to analyze bacterial communities associated with eight boreal moss species collected near Fairbanks, AK USA. We found that host identity was more important than site in determining bacterial community composition and that mosses harbor diverse lineages of potential N2- fixers as well as an abundance of novel taxa assigned to understudied bacterial phyla (including candidate phylum WPS-2). We performed shotgun metagenomic sequencing to assemble genomes from the WPS-2 candidate phylum and found that these moss-associated bacteria are likely anoxygenic phototrophs capable of carbon fixation via RuBisCo with an ability to utilize byproducts of photorespiration from hosts via a glyoxylate shunt. These results give new insights into the metabolic capabilities of understudied bacterial lineages that associate with mosses and the importance of plant hosts in shaping their microbiomes.

microbiology↗