Jonathan Shaw

Data access for the 1,000 Plants (1KP) project

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

Phylogeny and diversification of bryophytes

The bryophytes comprise three phyla of embryophytes that are well established to occupy the first nodes among extant lineages in the land-plant tree of life. The three bryophyte groups (hornworts, liverworts, mosses) may not form a monophyletic clade, but they share life history features including dominant free-living gametophytes and matrotrophic monosporangiate sporophytes. Because of their unique vegetative and reproductive innovations and their critical position in embryophyte phylogeny, studies of bryophytes are crucial to understanding the evolution of land plant morphology and genomes. This review focuses on phylogenetic relationships within each of the three divisions of bryophytes and relates morphological diversity to new insights about those relationships. Most previous work has been on the mosses, but progress on understanding the phylogeny of hornworts and liverworts is advancing at a rapid pace. Multilocus multigenome studies have been successful at resolving deep relationships within the mosses and liverworts, whereas single-gene analyses have advanced understanding of hornwort evolution.

Life history variation in gametophyte populations of the moss Ceratodon purpureus (Ditrichaceae)

The life cycles of mosses and other bryophytes are unique among land plants in that the haploid gametophyte stage is free-living and the diploid sporophyte stage is ephemeral and completes its development attached to the maternal gametophyte. Despite predictions that populations of haploids might contain low levels of genetic variation, moss populations are characterized by substantial variation at isozyme loci. The extent to which this is indicative of ecologically important life history variation is, however, largely unknown. Gametophyte plants from two populations of the moss Ceratodon purpureus were grown from single-spore isolates in order to assess variation in growth rates, biomass accumulation, and reproductive output. The data were analyzed using a nested analysis of variance, with haploid sib families (gametophytes derived from the same sporophyte) nested within populations. High levels of life history variation were observed within both populations, and the populations differed significantly in both growth and reproductive characteristics. Overall gametophytic sex ratios did not depart significantly from 1:1 within either population, but there was significant variation among families in both populations for progeny sex ratio. Some families produced predominantly male gametophytes, while others yielded predominantly females. Because C. purpureus has a chromosomal mechanism of sex determination, these observations suggest differential (but unpredictable) germination of male and female spores. Life history observations showed that male and female gametophytes are dimorphic in size, maturation rates, and reproductive output.

Potential for the Evolution of Heavy Metal Tolerance in Bryum argenteum, a Moss. I. Variation Within and Among Populations

Bryum argenteum frequently occurs in urban environments and therefore appears to have the ability to tolerate high levels of such atmospheric pollutants as lead. The presence of genetic variation for tolerance to lead was assessed within and among three populations of this species from Ithaca, New York state. Plants from these populations contained extremely different concentrations of lead and other metals, but there was little or no variation in metal tolerance among the populations. There were, however, significant differences in general vigor (growth rates across all experimental treatments) among populations. Moreover, the rural and suburban populations contained high levels of variation in vigor among haploid-sib families (families of gametophytes derived from different sporophytes). The urban population, in contrast, contained conspicuously less variation than the other two.

Electrophoretic evidence of reproductive isolation between two varieties of the moss, Climacium americanum

Two hundred and twenty individuals of the moss, Climacium americanum, from three localities in the Piedmont of North Carolina were sampled for a study of electrophoretically detectable genetic variation. Eight enzymes (ACP, ADH, ESTfl, GOT, PER, PGI, PGM, and SOD) were assayed and only two (GOT, SOD) were monomorphic at all three localities, in spite of the extreme rarity of sexual reproduction in this species. Although the var. kindbergii has generally been considered a form of C. americanum induced by submersion in water, there was a strong correlation between enzyme phenotypes and morphological characters distinguishing the two varieties of C. americanum. These data suggest that there is linkage disequilibrium among the loci coding for ACP, PGM, and PGI, and between these loci and those controlling several morphological characters that distinguish the two varieties of C. americanum.

Efficient purging of deleterious mutations in plants with haploid selfing

In diploid organisms, selfing reduces the efficiency of selection in removing deleterious mutations from a population. This need not be the case for all organisms. Some plants, for example, undergo an extreme form of selfing known as intragametophytic selfing, which immediately exposes all recessive deleterious mutations in a parental genome to selective purging. Here, we ask how effectively deleterious mutations are removed from such plants. Specifically, we study the extent to which deleterious mutations accumulate in a predominantly selfing and a predominantly outcrossing pair of moss species, using genome-wide transcriptome data. We find that the selfing species purge significantly more nonsynonymous mutations, as well as a greater proportion of radical amino acid changes which alter physicochemical properties of amino acids. Moreover, their purging of deleterious mutation is especially strong in conserved regions of protein-coding genes. Our observations show that selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale.

Disentangling knots of rapid evolution: origin and diversification of the moss order Hypnales

Abstract The Hypnales are the largest order of mosses comprising approximately 4200 species. Phylogenetic reconstruction within the group has proven to be difficult due to rapid radiation at an early stage of evolution and, consequently, relationships among clades have remained poorly resolved. We compiled data from four sequence regions, namely, nuclear ITS1–5·8S–ITS2, plastid trnL–F and rps4, and mitochondrial nad5, for 122 hypnalean species and 34 species from closely related groups. Tree topologies from both Bayesian and parsimony analyses resolve the order as monophyletic. Although inferences were made from fast-evolving genes, and despite strong phylogenetic signal in the nuclear ITS1–5·8S–ITS2 data, monophyly, as well as backbone nodes within the Hypnales, remains rather poorly supported except under Bayesian inferences. Ancestral distribution based on Bayesian dispersal-vicariance analysis supports a Gondwanan origin of the Hypnales and subsequent geographical radiation in the area of the former Laurasian supercontinent. Reconstruction of historical biogeography is congruent with mainly tropical and Gondwanan distributions in the sister groups Hypnodendrales, Ptychomniales, and Hookeriales, and with the dating for the oldest pleurocarp and hypnalean fossils. We contrast groupings in the phylogenetic tree with recent classifications and other phylogenetic inferences based on molecular data, and summarise current knowledge on the evolutionary history of, and relationships among, the Hypnales.

INTER- AND INTRASPECIFIC VARIATION OF MOSSES IN TOLERANCE TO COPPER AND ZINC

Bryophytes are often viewed as slowly evolving with little genetic variation within and among populations. A study of heavy‐metal tolerance was initiated to test the capacity of bryophytes to undergo genetic differentiation in response to natural selection.

Effects of Metals on Growth, Morphology, and Reproduction of Ceratodon purpureus

Gametophytic plants from six populations of the moss Ceratodon purpureus (Hedw.) Brid. were grown on substrates with varied degrees of heavy-metal contamination in order to assess the effects of metal pollution on growth, leaf size, and formation of archegonia and antheridia. Sex ratios and the overall levels of sexual expression varied greatly among samples from natural pop- ulations. Sex ratios in four populations were biased in favor offemales, one in favor of males, and one contained asexual gametophores only. Experimental substrates had a significant effect on the overall levels of sexual expression but not on the relative frequencies of male versus female stems. Innate differences in leaf size among populations were maintained in a common garden but leaf size was also affected by substrate. Patterns ofphenotypic plasticity characterizing the six populations were indistinguishable. Plants from several populations that originated in uncontaminated habitats grew as well on mine soil as plants from a mine-site population, suggesting an absence of ecotypic

Peristome Development in Mosses in Relation to Systematics and Evolution. IV. Haplolepideae: Ditrichaceae and Dicranaceae

The classification of mosses into subclasses and orders is based to a large extent on the morphology of the peristome teeth, yet little information exists on development of peristomes. In this paper we describe the sequences of cell divisions leading to peristome formation in six species of mosses representing two families with haplolepideous peristome structure. The earliest develop- mental stages conform to the pattern documented in other mosses and highlight the uniformity of these early stages among mosses of diverse relationship. Peristome development in haplolepideous mosses diverges from the pattern found in diplolepideous species when each of eight cells in the Inner Peristomial Layer undergoes anticlinal divisions. Haplolepideous species share a pattern of peristome development that appears to be unique to this group of mosses. Similarities in the ar- rangement of cells comprising mature haplolepideous peristomes and early stages of Bryum-type diplolepideous peristomes may indicate a relationship between these peristome types, or may be due in part to evolutionary convergence. Developmental evidence suggests that haplolepideous peristome teeth are homologous to the cilia of Bryum-type peristomes rather than to the endostome segments, as is commonly thought.