Our lab contributed to a phylogenomic reconstruction of the Sphagnopsida, which was published this past week: Shaw A.J., N. Devos, Y. Liu, C. J. Cox, B. Goffinet, K.I. Flatberg & B. Shaw. 2016. Organellar phylogenomics of an emerging model system: Sphagnum (peatmoss). Annals of Botany 118: 185–196.

The abstract reads: 

Background and Aims: Sphagnum-dominated peatlands contain approx. 30 % of the terrestrial carbon pool in the form of partially decomposed plant material (peat), and, as a consequence, Sphagnum is currently a focus of studies on biogeochemistry and control of global climate. Sphagnum species differ in ecologically important traits that scale up to impact ecosystem function, and sequencing of the genome from selected Sphagnum species is currently underway. As an emerging model system, these resources for Sphagnum will facilitate linking nucleotide variation to plant functional traits, and through those traits to ecosystem processes. A solid phylogenetic framework for Sphagnum is crucial to comparative analyses of species-specific traits, but relationships among major clades within Sphagnum have been recalcitrant to resolution because the genus underwent a rapid radiation. Herein a well-supported hypothesis for phylogenetic relationships among major clades within Sphagnum based on organellar genome sequences (plastid, mitochondrial) is provided.

Methods: We obtained nucleotide sequences (273 753 nucleotides in total) from the two organellar genomes from 38 species (including three outgroups). Phylogenetic analyses were conducted using a variety of methods applied to nucleotide and amino acid sequences. The Sphagnum phylogeny was rooted with sequences from the related Sphagnopsida genera, Eosphagnum and Flatbergium.

Key Results: Phylogenetic analyses of the data converge on the following subgeneric relationships: (Rigida (((Subsecunda) (Cuspidata)) ((Sphagnum) (Acutifolia))). All relationships were strongly supported. Species in the two major clades (i.e. Subsecunda + Cuspidata and Sphagnum + Acutifolia), which include >90 % of all Sphagnum species, differ in ecological niches and these differences correlate with other functional traits that impact biogeochemical cycling. Mitochondrial intron presence/absence are variable among species and genera of the Sphagnopsida. Two new nomenclatural combinations are made, in the genera Eosphagnum and Flatbergium.

Conclusions: Newly resolved relationships now permit phylogenetic analyses of morphological, biochemical and ecological traits among Sphagnum species. The results clarify long-standing disagreements about subgeneric relationships and intrageneric classification.

Rafa Medina has been an inspiring member of the lab since 2012, and is now moving to new adventures in Illinois at Augustana College. We will miss him and wish him much happiness and success.

The bioinformatic pipeline central to our ATOL pleurocarp and Funariaceae diversification studies is out:

Johnson M.G., E.M. Gardner, Y. Liu, R. Medina, B. Goffinet, A.J. Shaw, N.J.C. Zerega & N.J. Wickett. 2016. HybPiper: extracting coding sequence and introns for phylogenetics from high-throughput sequencing reads using target enrichment. Applications in Plant Sciences 4(7):1600016 (DOI: http://dx.doi.org/10.3732/apps.1600016) pdf

The abstract reads: Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high- throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user- friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae).
Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig as- sembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus.
Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.

The latest paper from the lab, highlighting Jessica’s work from her postdoc here was published in Frontiers in Plant Sciences: Budke J.M. & B. Goffinet. 2016. Comparative cuticle development in morphologically divergent mosses of the Funariaceae. Frontiers in Plant Sciences 7: 832. pdf (open access).

The abstract reads: The calyptra is a maternal structure that protects the sporophyte offspring from dehydration, and positively impacts sporophyte survival and fitness in mosses. We explore the relationship between cuticle protection and sporophyte height as a proxy for dehydration stress in Funariaceae species with sporophytes across a range of sizes. Calyptrae and sporophytes from four species were collected from laboratory-grown populations at two developmental stages. Tissues were embedded, sectioned, and examined using transmission electron microscopy. Cuticle thickness was measured from three epidermal cells per organ for each individual and compared statistically. All four species have cuticles consisting of a cuticle proper and a cuticular layer on the calyptra and sporophyte at both developmental stages. Across species, shorter sporophytes are associated with smaller calyptra and thinner calyptra cuticles, whereas taller sporophytes are associated with larger calyptra and thicker calyptra cuticles. Independent of size, young sporophytes have a thin cuticle that thickens later during development, while calyptrae have a mature cuticle produced early during development that persists throughout development. This study adds to our knowledge of maternal effects influencing offspring survival in plants. Released from the pressures to invest in protection for their sporophyte offspring, maternal resources can be allocated to other processes that support sporophyte reproductive success. Using a comparative developmental framework enables us to broaden our understanding of cuticle development across species and provides structural evidence supporting the waterproofing role of the moss calyptra.

In a new paper that came out today we report the cyanomorph of Ricasolia virens, and how this may shape our understanding of the evolution of photosymbiodemes in the Lobariaceae.

Tønsberg T., H. Blom, B. Goffinet, J. Holtan-Hartwig & L. Lindblom. 2016. The cyanomorph of Ricasolia virens comb. nov. (Lobariaceae, lichenized Ascomycetes). Opuscula Philolichenum 15: 12–21. The pdf should be available here.

The abstract reads: The cyanomorph and photosymbiodemes are here reported for the first time for Ricasolia virens (With.) H.H. Blom & Tønsberg comb. nov. (≡ Lobaria virens (With.) J.R. Laundon). The cyanomorph of R. virens is dendriscocauloid. The observed early developmental stages involve (1) a free-living cyanomorph and (2) a photosymbiodeme composed of the cyanomorph supporting small, foliose, chloromorphic lobes. Whereas the chloromorph continues to grow, the cyanomorph decays and disappears leading to the final stage (3), the free-living chloromorph. Secondary cyanomorphs emerging from the chloromorph are not known.

Laenen B., A. Machac, S.R. Gradstein, B. Shaw, J. Patiño, A. Désamoré, B. Goffinet, C.J. Cox, J. Shaw & A. Vanderpoorten. 2016. Increased diversification rates follow shifts to bisexuality in liverworts. New Phytologist 210: 1121–1129. pdf

The abstract reads: Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts.
We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests.
We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present.
Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism.

Earlier this winter, Rafael Medina was offered a tenure-track position at Augustana College. Rafa completed his dissertation at the Universidad Autónoma de Madrid in Spain, in Evolutionary Biology and Biodiversity. His dissertation was entitled: “Estudios de taxonomía integrativa en el género Orthotrichum Hedw., subgénero Pulchella” (Integrative taxonomy studies on the genus Orthotrichum, subgen. Pulchella). Apto Cum Laude. He then joined our lab to lead the phylogenomic reconstruction of the Funariales. Congratulations!

We are delighted to announce that Jessica (Budke) was offered and accepted a position a tenure-track position at the University of Tennessee, Knoxville where she will join the EEB department and will direct the UT Herbarium. Congratulations.

Jessica was co-advised by Dr. Cynthia Jones and Bernard Goffinet. She completed her MSc in 2006, presenting a thesis entitled “Peristome development and phylogenetic relationships of the moss Timmia megapolitana Hedw.” Her Ph.D. dissertation, “Examining the gametophytic calyptra and its role in sporophyte development of the moss Funaria hygrometrica Hedw.”, was presented in 2011. Jessica then moved to the University of California Davis were she held a Katherine Esau Postdoctoral Research Fellow.

Lily Lewis and Jessica Budke on a navy ship in the Beagle channel (Cape Horn)

Two publications with contributions from the lab were published this week.

1. The first analysis of transcriptomes of pleurocarpous mosses led by Matt Johnson (postdoc with norman Wickett in Chicago) appeared: Johnson M.G., C. Malle, B. Goffinet, A.J. Shaw & N.J. Wickett. 2016. A phylotranscriptomic analysis of gene family expansion and evolution in the largest order of pleurocarpous mosses (Hypnales, Bryophyta). Molecular Phylogenetics and Evolution 98: 29–40. (pdf)

 

The abstract reads: The pleurocarpous mosses (i.e., Hypnanae) are a species-rich group of land plants comprising about 6,000 species that share the development of female sex organs on short lateral branches, a derived trait within mosses. Many of the families within Hypnales, the largest order of pleurocarpous mosses, trace their origin to a rapid radiation less than 100 million years ago, just after the rise of the angiosperms. As a result, the phylogenetic resolution among families of Hypnales, necessary to test evolutionary hypotheses, has proven difficult using one or few loci. We present the first phylogenetic inference from high-throughput sequence data (transcriptome sequences) for pleurocarpous mosses. To test hypotheses of gene family evolution, we built a species tree of 21 pleurocarpous and six acrocarpous mosses using over one million sites from 659 orthologous genes. We used the species tree to investigate the genomic consequences of the shift to pleurocarpy and to identify whether patterns common to other plant radiations (gene family expansion, whole genome duplication, or changes in the molecular signatures of selection) could be observed. We found that roughly six percent of all gene families have expanded in the pleurocarpous mosses, relative to acrocarpous mosses. These gene families are enriched for several gene ontology (GO) terms, including interaction with other organisms. The increase in copy number coincident with the radiation of Hypnales suggests that a process such as whole genome duplication or a burst of small-scale duplications occurred during the diversification. In over 500 gene families we found evidence of a reduction in purifying selection. These gene families are enriched for several terms in the GO hierarchy related to ‘‘tRNA metabolic process.” Our results reveal candidate genes and pathways that may be associated with the transition to pleurocarpy, illustrating the utility of phylotranscriptomics for the study of molecular evolution in non-model species.

 

2. Vigalondo B., Y. Liu, I. Draper, F. Lara, R. Garilleti, V. Mazimpaka & B. Goffinet. 2016. Comparing three complete mitochondrial genomes of the moss genus Orthotrichum Hedw. Mitochondrial DNA Part B: Resources 1: 176–178. http://dx.doi.org/10.1080/23802359.2016.1149784.

The abstract reads: Here, we present a comparative analysis of the mitochondrial genome of three representatives of Orthotrichum Hedw (Bryophyta): two populations of O. diaphanum and one of the related species, namely O. macrocephalum. Their mitochondrial genomes share the same gene content and gene order, and are furthermore structurally identical to those of other arthrodontous mosses. The mitogenome of the allopatric samples of O. diaphanum differ in 0.1% of their sequence, with protein coding genes holding five mutations, including two non-synonymous changes. The divergence between the mitogenomes of the two species, O. diaphanum and O. macrocephalum, is 0.4%. Within a broader sampling of the Orthotrichaceae, patterns of genome divergence are consistent with phylogenetic relationships.

Dinah has been awarded a Summer Undergraduate Research Fellowship from UCONN to pursue her work on Dendriscocaulon and Ricasolia quercizans in North America. She joined our lab in the fall of 2014 and has been pursuing an independent study. She is spending the current semester abroad. Congratulations.