Current projects:

Liverwort tree of life: a collaborative project involving six institutions aimed at reconstructiong the evolutionary of liverworts through the integration of morphological, ultrastructural, sequence and genomic characters. Read more ...….

Entomophily in the dung mosses: insects are the vector for spore dispersal in only one family of mosses, the Splachnaceae. Indeed about half of the 70 or so species attract flies using olfactory and visual cues to recruit them to disperse their spores. How? Read more ...…

Systematics of Peltigera (lichenized Ascomycetes): Species concept in the lichen-forming fungal genus Peltigera are notoriously labile, due to extensive morphological and chemical diversity across broad geographical areas. We continue to collaborate on regional revisions, and are currently completing treating the taxa occurring in New Guinea.  Read more ...

Student projects:

The moss calyptra and its influence on sporophyte development (Ph.D. project by Jessica Budke). Read more....

The phylogenetic history and population genetics of hornwort Megaceros aenigmaticus (Ph.D. project by Juan Carlos Villarreal).

Ongoing projects:

Moss phylogeny and phylogenetic diversity: This collaborative project with Jon Shaw (Duke University) focused on reconstructing the phylogeny of mosses based on sequences from three loci distributed across all three genomes, for one representative of each genus of mosses, and to test hypotheses pertaining to the distribution of diversity , in particular phylogenetic diversity in mosses. Read more…

Systematics of Orthotrichaceae: This diverse family of mosses comprises two main clades, differing primarily in the distribution of sex organs but also in their predominant geographical distribution. Our focus continues to be on the systematics of the genus Orthotrichum and in particular its segregation from its close relative Ulota. Read more….

Symbiont shift in lichens: Although most lichen-forming ascomycetes establish a close association with either a green alga or a cyanobacterium, some taxa and particularly members of the Peltigerales, may engage in a dual symbiosis, and moreover, shift their preference for either one as the primary symbiont, and form a lichen with solely with the cyanbacterium, or with the green algae and the cyanobacterium. This assumes it is indeed the same fungus. Read more…

Liverwort Tree of Life

NSF funded project — ATOL: Collaborative Research - Assembling the Liverwort Tree of Life: A Window into the Evolution and Diversification of Early Land Plants (Jan. 2006 until Dec. 2010).

This collaborative project (link to collaborators) project aims at resolving the liverwort Tree Of Life. Evidence accumulates that liverworts (Phylum Marchantiophyta) were among the first green plants to diversify on land some 500,000 million years ago and as such they represent the closest extant relative of the early of land plants. This species-rich group of small green plants is remarkably diverse in structure, and includes extremely ancient relictual lineages as well as more recent radiations of closely related species. The antiquity of liverworts and the rich biodiversity at all taxonomic levels provide an unparalleled window into early land plant diversification. This collaborative effort brings together experts from around the world for a multidisciplinary, highly integrated approach that combines anatomical and developmental features with DNA sequence and genome structural characters to resolve phylogenetic relationships across the entire spectrum of liverwort diversity. Three general types of data will be compiled: 1) conservative morphological and genome characters to resolve deep "backbone" relationships, 2) anatomical/developmental data to resolve intermediate-depth lineages, and 3) morphological and DNA sequence characters to resolve relationships among a sample of 800 taxa representing all genera of liverworts. A second major goal of the project is to integrate phylogenetic inferences and bionformatic efforts between this and other on-going NSF-supported projects, including several funded ATOL programs. These integrative activities include contributions to studies of genome structure and evolution across land plants, expansions of novel informatic tools to make methods, results, and implications widely accessible, and continued development of DNA sequence utilities that will benefit a broad range of scientists working on diverse organisms.

For more information regarding the project and its PIs go to ALiTOL homepage. The site offers links to resources for educators and students, and to access more information regarding the morphology, phylogeny, classification, and ecology of liverworts.

This collaborative project involves researchers from several institutions, each with a distinct contribution. Our laboratory focuses on the organization of the chloroplast genome. We aim at a) reconstructing the complete sequence of the chloroplast genome of representatives of major lineages of liverworts and b) testing for the phylogenetic significance of structural characters, such as gene inversion, gene deletion and translocation.

Collaborators:

Dr. A. Jonathan Shaw (Duke University) is the lead PI on this project. His efforts focus on sequencing multiple genes from all three genomic compartments for a representative of all (if possible) genera of liverworts.

Dr. Karen Renzaglia (Southern Illinois University) is describing the ultrastructure of a set of selected taxa.

Drs. Barbara Crandall-Stotler and Ray Stotler (Southern Illinois University) will score morphological characters for a set of liverwort taxa.

Dr. Yin-Long Qiu (University of Michigan) will survey liverwort taxa for structural rearrangements in the mitochondrial genome and the distribution of introns in mt genes, in search of phylogenetic markers.

Dr. Nico Cellinese and Reed Beaman (University of Florida) lead the bioinformatics efforts aimed at integrating the information and the results from all collaborating research laboratories.

Dr. John Engel and Matt von Konrat from the Field Museum in Chicago, two experts in the taxonomy of liverworts, verify the identity of all samples used in this project.

 

Mosses

Entomophily in mosses

Moss phylogenetic diversity

Systematics of Orthotrichaceae

 

Entomophily in mosses or “Dung is a great habitat but the rent may be too high”
The dung mosses distinguish themselves from other mosses not merely by their habitat but rather by their spore dispersal vector. Indeed virtually all other mosses rely on wind to disperse the spores released from the capsule. In Splachnum and related genera, the sporophyte is typically brightly colored and emits odors that attract flies. Not any kind of flies, but coprophilous flies that seek fresh dung and carcasses to feed and deposit their eggs. Upon landing on the sporophyte, the flies come in contact with the mass of sticky spores, which adhere to the body of the visitor. The flies realizing that they are deceived, take off in search of a suitable “substrate”. When they land on fresh dung or walks over decaying flesh, spores may fall off their body. The dung mosses thereby insure to be the first tenant; the spores germinate rapidly, and gametophytes quickly occupy the habitat.

Our research has focused on reconstructing the phylogenetic relationships among insect and wind dispersed members of the family in order to understand the evolutionary trends that led to the diversity of spore dispersal mechanisms. Species of Splachnum and Tetraplodon rely on flies. Other species, keep their spores inside the capsule until the capsule wall is broken by trampling animals. Many species of Tayloria rely on wind! Our phylogenetic reconstruction (Goffinet et al. 2004; Ame. J. Bot. pdf) suggests that neither mode of dispersal defines a monophyletic group, and hence that multiple shifts have occurred between wind and animal dispersal. What continues to elude us is what the ancestral condition was!

We are currently developing a collaborative project with Dr. Robert Raguso and Dr. Paul Marino. Dr. Raguso seeks to unravel the chemical diversity of the odors produced by entomophilous Splachnaceae. Dr. Marino aims at testing the power of distinct chemical in attracting various groups of flies. Together we hope to reconstruct the evolutionary history of the Splachnaceae and in particular the patterns of its morphological and chemical diversification. Thanks to a grant from the National Geographic Society, we have complete preliminary field studies in Alaska and Patagonia. Two Chilean students of the University of Magallanes in Punta Arenas currently describe the fauna that visit two unrelated species of Tayloria (i.e., T. miralibis and T. dubyi, see photos here). See some pictures from these trips.

Moss phylogenetic diversity project:
This collaborative project was led by Dr. Jonathan Shaw from Duke University and also involved Dr. Cymon Cox who is now at the British Museum of Natural History.

The objective of the project were a) to sequence three loci, one from each genome (i.e., rps4 [cpDNA], nad5 [mtDNA] and 26S-LSU [nDNA]) from one representative from every genus of mosses (approximately 800 taxa), b) provide phylogenetic inferences for mosses and c) infer patterns of phylogenetic diversity in mosses.

Overview of achievements:

We have compiled data matrices for all three loci that included rps4, nad5 and 26S sequences, with the vast majority of sequences newly generated during this project (i.e., 536, 518 and 578 respectively, for a total of 1632 new sequences), by the two laboratories. All sequences are being submitted to GenBank (rps4 and nad5 already deposited).

We also extended the sampling to other loci for specific taxa to address systematic hypotheses: Vittiaceae (Vanderpoorten et al. 2002), Orthotrichaceae (Goffinet et al. 2004a), Splachnaceae (Goffinet et al. 2004b), Hookeriales (Buck et al. 2004), Hypopterygiaceae (Shaw et al. in prep.), Brachytheciastrum (Vanderpoorten et al. 20005) Sematophyllaceae (Goffinet et al. in prep.) and Pottiaceae (Quandt et al. in prep.).

Patterns in rate of radiation were critically examined within the pleurocarpous mosses (Shaw et al. 2003) based on sampling by Buck et al. (2000).

An extensive sampling of characters (8 loci) for 30 representatives of major lineages of mosses led to a robust hypothesis for the backbone phylogeny of mosses (Cox et al. 2004).

This phylogeny, complemented by those focused on orders and families of served as a basis for the revision of the classification of genera of the Bryophyta (Goffinet & Buck 2004).

A generic phylogeny of mosses is being reconstructed based on all rps4, nad5 and 26S sequences (Cox et al. in prep.) and inferences from rps4 and nad5 were used to examine patterns of variation in phylogenetic diversity along a geographic gradient (Shaw et al. 2005).

The backbone phylogeny was also used to reconstruct the history of the loss of the rpoA gene from the chloroplast genome of mosses (Goffinet et al. 2005), and currently serves as the phylogenetic hypothesis upon which significance of the reversal of a 74kb fragment of the single copy unit of the chloroplast genome is reconstructed (Goffinet et al. in prep.).

Summary of major publications emanating from grant support research:

Shaw A.J., C. J. Cox, B. Goffinet, & W. R. Buck.  2003. Phylogenetic evidence of a rapid radiation of pleurocarpous mosses (Bryophyta).  Evolution 57: 2226-2241. pdf.

Pleurocarpous mosses, characterized by lateral female gametangia and highly branched, interwoven stems, comprise three orders and some 5000 species, or almost half of all moss diversity.  Recent phylogenetic analyses resolve the Ptychomniales as sister to the Hypnales plus Hookeriales.  Species richness is highly asymmetric with approximately 100 Ptychomniales, 750 Hookeriales, and 4400 Hypnales.  Chloroplast DNA sequences were obtained to compare partitioning of molecular diversity among the orders with estimates of species richness, and to test the hypothesis that either the Hookeriales or Hypnales underwent a period (or periods) of exceptionally rapid diversification. Levels of biodiversity were quantified using explicitly historical "phylogenetic diversity" and nonhistorical estimates of standing sequence diversity. Diversification rates were visualized using lineage-through-time (LTT) plots and statistical tests of alternative diversification models were performed using the methods of Paradis (1997).  The effects of incomplete sampling on the shape of LTT plots and performance of statistical tests were investigated using simulated phylogenies with incomplete sampling.  Despite a much larger number of accepted species, the Hypnales contain lower levels of (cpDNA) biodiversity than its sister group, the Hookeriales, based on all molecular measures. Simulations confirm previous results that incomplete sampling yields diversification patterns that appear to reflect a decreasing rate through time, even when the true phylogenies were simulated with constant rates.  Comparisons between simulated results and empirical data indicate that a constant rate of diversification cannot be rejected for the Hookeriales.  The Hypnales, however, appear to have undergone a period of exceptionally rapid diversification for the earliest 20% of their history.

Cox C.J., B. Goffinet, A.J. Shaw, & S. Boles. 2004. Phylogenetic relationships among the mosses based on heterogeneous bayesian analysis of multiple genes from multiple genomic compartments.  Systematic Botany 29: 234-250. pdf.

Nucleotide sequences from eight nuclear, chloroplast, and mitochondrial genes were obtained from 30 mosses (plus four outgroup liverworts) in order to resolve phylogenetic relationships among the major clades of division Bryophyta.  Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood (ML), and Bayesian inference.  Inferences were compared from Bayesian analyses using homogeneous and several heterogeneous models.  Estimates of clade confidence were based on bootstrap analyses, posterior probabilities (in Bayesian analyses) and novel combined approaches. Most ingroup relationships were congruent among analyses, but support for individual clades depended on the analytical approach. Increasingly parameterized models of nucleotide substitution in the likelihood analyses provided significantly higher goodness-of-fit to the data. The results suggest that 1) the Bryophyta, including Sphagnum and Takakia, are monophyletic, 2) Andreaea and Andreaeobryum form a monophyletic group, 3) Oedipodium griffithianum is sister to all other operculate taxa, 4) mosses with nematodontous peristomes are paraphyletic and basal to arthrodontous mosses, 5) Diphyscium is sister to all other arthrodontous mosses, 6) Encalypta is sister to the Funariaceae, and 6) mosses with diplolepideous-alternate peristomes form a monophyletic group. Implications of the phylogenetic hypothesis for morphological evolution in mosses include 1) a pseudopodium has arisen independently in Sphagnum and Andreaea, 2) the mucilage hairs of Andreaeobryum and Takakia are non-homologous, 3) the stomata found in Sphagnum are not homologous to those of other mosses, and 4) that stomata were absent in the ancestor of all mosses.

Shaw, A.J., C.J. Cox, & B. Goffinet. 2005. Global patterns of moss diversity: taxonomic and molecular inferences. Taxon 54: 337-352. pdf.

Taxonomic and molecular data were utilized to test the hypothesis that moss diversity is greatest near the equator.  Species richness estimates from 86 taxonomic checklists representing global moss diversity do not support the hypothesis that, in general, mosses are more species-rich in the tropics than at higher latitudes. A significant latitudinal gradient was, however, detected for North, Central, and South American samples when analyzed alone.  Taxonomic estimates of biodiversity patterns were compared to molecular estimates based on standing nucleotide diversity, and on phylogenetic diversity, the latter taking into account the historical information contained in a molecular phylogenetic tree for the mosses.  Molecular estimates suggest that moss diversity is highest in the Southern Hemisphere and lowest in the Northern Hemisphere, with the tropics having an intermediate level.  The differences, however, are slight, and analyses of molecular variance (AMOVA) indicate that there is virtually no generalized differentiation between major latitudinal zones.  These results reflect that fact that virtually all moss lineages have representatives in all three latitudinal zones.  At the nucleotide level, mosses best fit the pattern of “everything is everywhere”.

Goffinet B., & W.R. Buck.  2004. Systematics of Bryophyta: from molecules to a revised classification. Monographs in Systematic Botany from the Missouri Botanical Garden 98: 205-239.

Two hundred years of bryological investigations of morphological, anatomical and developmental characters form the foundation for systematics concepts in mosses, and hence for their classification. With the development of phylogenetic theory and more recently of techniques allowing the extraction of DNA and the amplification and sequencing of specific loci, a new source of characters has become available to test systematic hypotheses. In the last decade over 100 phylogenetic studies of mosses have been published. These have led to the revision of many supraspecific taxonomic circumscriptions.  Indeed, many taxa, whether these are genera, families or orders, have been shown to be paraphyletic or polyphyletic. The revised lineages may satisfy a criterion of monophyly, but in some cases they can no longer be diagnosed using traditional morphological characters. Although phylogenetic inferences are shaping our systematic concepts, the significance of the contributions remains to be tested by future studies.  Indeed, several new hypotheses are only weakly supported.  Only recently have inferences been made from multiple loci spanning all three genomic compartments, and structural constraints on the evolution of molecules are only beginning to be integrated in analytical assumptions.  Here we review most studies that have addressed systematic hypotheses and, based on these results, have amended our recent classification of mosses.  The following new taxa are proposed: Takakiopsida (Crandall-Stotler) comb. et stat. nov., Andreaeaobryopsida (B. M. Murray) comb. et stat. nov., Oedipodiopsida (Schimp.) comb. et stat. nov., Oedipodiales (Schimp.) comb. et stat. nov., Tetraphidopsida (M. Fleisch.) comb. et stat. nov., Scouleriales (S. P. Churchill) comb. et stat. nov., Bryanae (Engl.) comb. et stat. nov., Rhizogonianae (M. Fleisch.) comb. et stat. nov., Rhizogoniales (M. Fleisch.) comb. et stat. nov., and Pylaisiadelphaceae fam. nov.

Goffinet B., N.J. Wickett, A. J. Shaw & C. J. Cox. 2005. Phylogenetic significance of the rpoA loss in the chloroplast genome of mosses. Taxon 54: 353-360. pdf.

A recent survey of arthrodontous mosses revealed that their chloroplast genome lacks the gene encoding the alpha subunit of the RNA polymerase (i.e., rpoA), and that at least in Physcomitrella patens the gene has been transferred to the nuclear genome. Subsequently the gene was recorded from the cytoplasmic genome in Takakia and Sphagnum. Here we extend the survey to representatives of all major lineages of mosses to determine when in the evolutionary history of the Bryophyta the loss took place. Amplifications using primers annealing to the flanking regions of the rpoA gene yield a product that contains the gene in Takakia, Sphagnum, Andreaea, Oedipodium, Polytrichaceae, and Buxbaumia. The gene is lacking in all arthrodontous mosses, including Diphyscium but also in both species of Tetraphis. Reconstruction of the transfer on the phylogeny of mosses suggests a) that the rpoA gene was lost twice and b) that the gene was lost after the divergence of the Buxbaumiidae and prior to the divergence of Diphyscium from the remaining Bryopsida.

Buck, W.R., C.J. Cox, A.J. Shaw, & B. Goffinet. 2004 (2005). Ordinal relationships of pleurocarpous mosses, with special emphasis on the Hookeriales.  Systematics and Biodiversity 2: 121-145. pdf.

Sequence data from four DNA regions, namely, chloroplast trnL–trnF and rps4, mitochondrial nad5, and nuclear 26S rDNA, were surveyed from 89 taxa traditionally associated with the Hookeriales, five Hypnales and five outgroups. Phylogenetic reconstruction was performed using the maximum parsimony and maximum likelihood optimality criteria, and by Bayesian phylogenetic inference. Thirteen morphological characters were optimized on the resulting phylogeny using maximum likelihood. Inferences of character evolution based on the molecular phylogeny suggest that 1) the core of pleurocarpous mosses (i.e., the Hypnanae) is best defined and thus distinguished from the Ptychomnianae by smooth rather than furrowed capsules, 2) a synapomorphy for the Ptychomnianae is the short and double (or absent) costa, and 3) the Hookeriales are defined by undifferentiated alar cells. The Ptychomniaceae plus Garovagliaceae are recognized as a single family in its own order, the Ptychomniales ord. nov. and superorder, the Ptychomnianae, superord. nov. This superorder is sister to the combined Hypnales and Hookeriales, i.e., the Hypnanae. The Hookeriales are interpreted as consisting of seven families, the Hypopterygiaceae, Saulomataceae fam. nov., Daltoniaceae, Schimperobryaceae fam. nov., Hookeriaceae, Leucomiaceae and Pilotrichaceae. The Adelotheciaceae are embedded within the Daltoniaceae and considered synonymous with that family. Within the Ptychomniaceae, Ptychomniella is raised from a subgenus of Ptychomnion to generic status. Euptychium setigerum and its monospecific section, Crassisubulata, are transferred to Garovaglia. Callicostella diatomophila is transferred to Diploneuron. Additional alterations at the generic level await more data.

Goffinet, B., N. Wickett, O. Werner, R.M. Ros, A.J. Shaw & C.J. Cox. 2007. Distribution and phylogenetic significance of a 71 kb inversion in the chloroplast genome of the Funariidae (Bryophyta). Annals of Botany 99: 747-753. pdf.

Background and aims The recent assembly of the complete sequence of the plastid genome of the model taxon Physcomitrella patens (Funariaceae, Bryophyta) revealed that a 71kb fragment, encompassing much of the large single copy (LSC) region, is inverted. This inversion of 57% of the genome is the largest rearrangement detected in the plastid genomes of plants to date. Although initially considered diagnostic of Physcomitrella patens, the inversion was recently shown to characterize the plastid genome of two species from related genera within Funariaceae, but was lacking in another member of Funariidae. The phylogenetic significance of the inversion has remained ambiguous. Methods We survey exemplars of all families included in Funariidae. We amplified DNA sequences spanning the inversion break ends, using primers that anneal to genes on either side of the putative end points of the inversion. Primer combinations were designed to yield a product for either the inverted or the non-inverted architecture. Key results Our survey reveals that exemplars of eight genera of Funariaceae, the sole species of Disceliaceae and three generic representatives of Encalyptales all share the 71kb inversion in the LSC of the plastid genome. By contrast, the plastid genome of Gigaspermaceae (Funariales) is characterized by a gene order that congruent with that described for other mosses, liverworts and hornworts, and hence it does not possess this inversion. Conclusion The phylogenetic distribution of the inversion in the gene order supports a hypothesis only weakly supported by inferences from sequence data whereby Funariales are paraphyletic, with Funariaceae and Disceliaceae sharing a common ancestor with Encalyptales, and Gigaspermaceae sister to this combined clade. To reflect these relationships, Gigaspermaceae are excluded from Funariales and accommodated in their own order, the Gigaspermales order nov. within Funariideae.

For further information on the Moss Phylogenetic Diversity project is provided by Jon Shaw at http://www.biology.duke.edu/bryology/mdp.html

Systematics of the Orthotrichaceae
To be completed

 

Lichens

Systematics of the lichen-forming genus Peltigera (Ascomycota).

Species concept in the lichen-forming fungal genus Peltigera are notoriously labile, due to extensive morphological and chemical diversity across broad geographical areas. In collaborations with Emmanuël Sérusiaux (University of Liège), Trevor Goward (University of British Columbia) and Jolanta Miadlikowska (Duke University) the species diversity has been revised for part of Western Europe (Goffinet et al. 1993), and Western Canada (Alberta by Goffinet & Hastings 1994, and British Columbia by Goward et al. 1995). Species concepts drawn from patterns in morphological character variation are tested against patterns in variation in DNA sequences, and have led to the desription of several new taxa (Goffinet & Miadlikowska 1998; Goward & Goffinet 1998; Goffinet et al. 2004). We are currently completing the revision of the species occurring in Papua New Guinea.

Although morphological and chemical characters continue to offer important foundations for systematic and phylogenetic hypotheses, ecological and geographic distribution often hint at genetically differentiated entities, despite morphological and chemical similarity. In some cases, the inability to distinguish two individuals contrasts with their resolution in two distinct clades of the phylogenetic tree. Such incongruence still requires an explanation. Alternatively, morphologically strikingly dissimilar populations may share identical DNA sequences, suggesting that either species are morphologically highly variable or that in some cases, cladogenesis is recent, and has not yet become translated in differentiation in the investigated loci.

We are currently examining the diversity of the genus in Central Africa and Macaronesia.

Shifts in symbiotic preferences (The lichen version of diversifying your investment portfolio)

Multiple symbioses in the Peltigerales: Various members of the Peltigerales distinguish themselves by their ability to form a lichen with a green alga and a cyanobacterium. If the photobionts contribute to a single thallus, the green alga is typically the primary symbiont and the cyanobacterium a secondary symbiont confined to internal or external structures called cephalodia. Under certain environmental circumstances, the fungus may establish an association only with the cyanobacterium. The two so-called morphotypes or phototypes thus involve the same fungus (See Goffinet & Bayer 1997) but in one the green alga is primary photobiont whereas in the other the cyanobacterium takes over that role to the exclusion of the green alga. The alternative symbioses may led to morphologically similar or completely dissimilar thalli; in all cases known it seems that at least the two associations differ in their secondary chemistry which is typically less complex in the cyanobacterial lichen.

Dendriscocaulonis characterized by its shrubby thalli that involve a cyanobacterium. None of the species is known to produce apothecia. In fact, the species are hypothesized to represent alternative symbiotic associations to the fungus-green alga association. Lobaria amplissima,for example, is lichenized primarily with a green alga, with cyanobacteria hidden in internal cephalodia. In western Europe, shrubby outgrowth emerge from the green thallus, and these only comprise the cyanobacterium. IN Western North America, free living lichens resembling these outgrowths are commonly found in moist forest environments.Their affinities have remained obscur. We have now sampled all known North American populations of Dendriscocaulon and estimated the haplotype diversity based on ITS sequence data. This project, which is a collaborative effort with Trevor Goward (Uni. British Columbia) and Dr. Tør Tønsberg (Uni. Bergen, Norway) also reconstruct the phylogenetic affinities of these populations. So far, the North American populations are scattered across five distinct lineages. More about this when we have completed the project!

 

Hornworts

Visit Juan Carlos' website for more details!

College of Liberal Arts and Sciences

Ecology and Evolutionary Biology