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.

Charlie was awarded $500 (Anderson & Crum Award) from the American Bryological and Lichenological Society for his fieldwork in the NorthEast to collect Physcomitrium pyriforme. Congratulations.

Two new studies from the lab have been published:

The first is part of Lily’s dissertation and focuses on comparisons of entire organellar genomes and the nuclear rDNA repeat among populations of Tetraplodon fuegianus in the Cape Horn Region:  Lewis, L., Y. Liu, R. Rozzi & B. Goffinet. 2016. Infraspecific variation within and across complete organellar genomes and nuclear ribosomal repeats in a moss. Molecular Phylogenetics and Evolution 96: 195–199. doi:10.1016/j.ympev.2015.12.005  pdf Google Scholar

The abstract reads: Bryophytes (mosses, liverworts, and hornworts) are diverse and ecologically and evolutionarily significant yet genome scale data sets and analyses remain extremely sparse relative to other groups of plants, and are completely lacking at the infraspecific level. By sequencing the complete organellar genomes and nuclear ribosomal repeat from seven patches of a South American sub-Antarctic neo-endemic non-model moss, we present the first characterization of infraspecific polymorphism within and across the three genomic compartments for a bryophyte. Diversity within patches is accounted for by both intraindividual and interindividual variation for the nuclear ribosomal repeat and plastid genome, respectively. This represents the most extensive infraspecific genomic dataset generated for an early land plant lineage thus far and provides insight into relative rates of substitution between organellar genomes, including high rates of nonsynonymous to synonymous substitutions.

The other studies is a phylogegraphic analysis of Bryoxiphium, a genus of scattered distribution in the Northern Hemisphere, with disjunct occurrences on Mauritius: Patiño, J., B. Goffinet, M. Sim-Sim & A. Vanderpoorten. 2016. Is the sword moss (Bryoxiphium) a preglacial Tertiary relict? Molecular Phylogenetics and Evolution 96: 200–206. doi:10.1016/j.ympev.2015.12.004 pdf  Google Scholar

The abstract reads: The disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium, exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes.

 

A further outcome of the Liverwort Tree of Life project is the study by Laenen et al., which was released today on-line. The study is entitled “Increased diversification rates follow shifts to bisexuality in liverworts” and is published in the  New Phytologist. [pdf]

 

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.

A new article about the work Lily and Bernard have been involved in in the Cape Horn Biosphere Reserve: Rozzi R., L. Lewis, F. Massardo & B. Goffinet. 2015. Luupidega ökoturism samblafloora väärtustamiseks: ülekutse Lõunast. [Ecotourism with a hand-lens to appreciate the bryoflora: an invitation from the South.] Samblasõber 18: 2–13. http://www.botany.ut.ee/bruoloogia/Rozzi.etal.SS.2015.pdf

After almost six years in EEB and our lab, Lily packed her books, cleaned her desk and moved to Chile, to  assist with the Tracing Darwin’s Path course and work with Ricardo Rozzi until April. Happy travels.

The early on-line version of the publication in Plant Biology:

Magdy M., O. Werner, S.F. McDaniel, B. Goffinet & R.M. Ros. 2015. A genomic scanning using AFLP to detect loci under selection in Funaria hygrometrica Hedw. along a climatic gradient in the Sierra Nevada mountains (Spain). Plant Biology (in press). doi:10.1111/plb.12381

is now available.

The abstract reads:

The common cord moss Funaria hygrometrica has a worldwide distribution and thrives in a wide variety of environments. Here, we studied the genetic diversity in F. hygrometrica along an abiotic gradient in the Mediterranean high mountain of Sierra Nevada (Spain) using a genome scan method. Eighty-four samples from 17 loca- tions from 24 to 2700 m were fingerprinted based on their amplified fragment length polymorphism (AFLP) banding pattern. Using PCA and Bayesian inference we found that the genetic diversity was structured in three or four clusters, respectively. Using a genome scan method we identified 13 outlier loci, which showed a signature of posi- tive selection. Partial Mantel tests were performed between the Euclidean distance matrices of geographic and climatic variables, versus the pair-wise genetic distance of the AFLP dataset and AFLP-positive outliers dataset. AFLP-positive outlier data were significantly correlated with the gradient of the climatic variables, suggesting adaptive variation among populations of F. hygrometrica along the Sierra Nevada Mountains. We highlight the additional analyses necessary to identify the nature of these loci, and their biological role in the adaptation process.