Bernard Goffinet

Evolution of the major moss lineages: phylogenetic analyses based on multiple gene sequences and morphology

Abstract Evolutionary relationships of mosses are still poorly understood, with family, order, and subclass circumscription and relationships remaining especially obscure. Over the past decade, a considerable body of data has accumulated, including information on morphological, developmental, anatomical, and ultrastructural characteristics, as well as nucleotide sequences for a number of nuclear and plastid genes. We have combined data from these different sources to provide an overview of the relationships of the major lineages of mosses. We analyzed a data set that includes 33 moss species and ten outgroup taxa drawn from the liverworts, hornworts, and vascular plants. Molecular data consisted of nucleotide sequences from four DNA regions, (rbcL, trnL-trnF, rps4 and 18S). Morphological data included 41 characters of which many were derived from published anatomical and ultra-structural studies. Combining morphological and molecular data in the analyses showed that mosses, including Sphagnum, Takakia, Andreaea and Andreaeobryum, form a monophyletic group, provided improved resolution of higher level relationships, and further insight into evolutionary patterns in morphology.

Phylogenetic Relationships among the Mosses Based on Heterogeneous Bayesian Analysis of Multiple Genes from Multiple Genomic Compartments

Abstract 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.

PHYLOGENETIC EVIDENCE OF A RAPID RADIATION OF PLEUROCARPOUS MOSSES (BRYOPHYTA)

Abstract 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 (cpDNA) 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 non‐historical 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 their 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.

Phylogenetic Relationships Among the Diplolepideous-alternate Mosses (Bryidae) Inferred from Nuclear and Chloroplast DNA Sequences

Abstract The diplolepideous-alternate peristome, when most highly developed, has endostome segments attached to a basal membrane and positioned alternate to the outer exostome teeth, with cilia often present between the segments. This peristome type defines the Bryidae ( sensu Vitt et al. 1998), which includes four orders: the Bryales, Leucodontales, Hypnales, and Hookeriales, of which the latter three are mainly pleurocarpous in their growth form. Chloroplast (rbcL, rps4, and trnL-trnF) and nuclear (18S rRNA) gene sequences have been analyzed using the parsimony optimality criterion to elucidate relationships among the Bryidae. The analyses strongly support the paraphyly of the Bryidae, with the Splachnidae, and possibly the Orthotrichidae, having arisen from ancestors within the Bryidae. The Leucodontales, Hypnales, and Hookeriales form a monophyletic group, as do the pleurocarpous members of the Bryidae. However, the two pleurocarpous clades are not resolved as sister groups, although their non-monophyly is not supported by the bootstrap. The phylogenetic hypothesis provides a context in which to infer evolutionary transitions in some key morphological characters relating to the peristome and the transition from the acrocarpous to pleurocarpous growth forms.

Circumscription and phylogeny of the Orthotrichales (Bryopsida) inferred from RBCL sequence analyses

The affinities as well as the circumscription of the Orthotrichaceae (Bryopsida), one of the most diverse families of mosses, have been the focus of a controversy for much of the last century. We obtained rbcL sequences for 37 arthrodontous mosses, including 27 taxa of the Orthotrichales. The sequences were analyzed using maximum parsimony and neighbor joining in order to (1) test the monophyly of the Orthotrichales and the Orthotrichaceae; (2) determine their phylogenetic relationships; and (3) test the current subfamilial classification within the Orthotrichaceae. Both analyses suggest that the Orthotrichales are polyphyletic. The Erpodiaceae and the Rhachitheciaceae as well as Amphidium and Drummondia, two genera of the Orthotrichaceae, are shown to be of haplolepideous affinity. The Splachnales, the Bryales sensu lato, and the Orthotrichales form a monophyletic clade sister to the Haplolepideae. Both neighbor joining and maximum parsimony also suggest that the Orthotrichaceae are composed of two major lineages dominated either by acrocarpous or cladocarpous taxa. The monophyly of the family is, however, only well supported by Tamuras distances. The genera Macrocoma, Macromitrium, Orthotrichum, Ulota, and Zygodon all appear to be artificial assemblages. This study illustrates the contribution of rbcL sequence data to bryophyte systematics and, particularly, in determining the affinities of taxa lacking a peristome, whose characters are central to the classification of mosses.

Changing lenses to assess biodiversity: patterns of species richness in sub-Antarctic plants and implications for global conservation

Article discussing patterns of species richness in sub-Antarctic plants and implications for global conservation.

Extant diversity of bryophytes emerged from successive post-Mesozoic diversification bursts

Unraveling the macroevolutionary history of bryophytes, which arose soon after the origin of land plants but exhibit substantially lower species richness than the more recently derived angiosperms, has been challenged by the scarce fossil record. Here we demonstrate that overall estimates of net species diversification are approximately half those reported in ferns and ∼30% those described for angiosperms. Nevertheless, statistical rate analyses on time-calibrated large-scale phylogenies reveal that mosses and liverworts underwent bursts of diversification since the mid-Mesozoic. The diversification rates further increase in specific lineages towards the Cenozoic to reach, in the most recently derived lineages, values that are comparable to those reported in angiosperms. This suggests that low diversification rates do not fully account for current patterns of bryophyte species richness, and we hypothesize that, as in gymnosperms, the low extant bryophyte species richness also results from massive extinctions.

Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-usage Bias

Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models.

Global patterns of moss diversity: taxonomic and molecular inferences

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 the 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”.

Mapping Uncertainty and Phylogenetic Uncertainty in Ancestral Character State Reconstruction: An Example in the Moss Genus Brachytheciastrum

The evolution of species traits along a phylogeny can be examined through an increasing number of possible, but not necessarily complementary, approaches. In this paper, we assess whether deriving ancestral states of discrete morphological characters from a model whose parameters are (i) optimized by ML on a most likely tree; (II) optimized by ML onto each of a Bayesian sample of trees; and (III) sampled by a MCMC visiting the space of a Bayesian sample of trees affects the reconstruction of ancestral states in the moss genus Brachytheciastrum. In the first two methods, the choice of a single- or two-rate model and of a genetic distance (wherein branch lengths are used to determine the probabilities of change) or speciational (wherein changes are only driven by speciation events) model based upon a likelihood-ratio test strongly depended on the sampled trees. Despite these differences in model selection, reconstructions of ancestral character states were strongly correlated to each others across nodes, often at r > 0.9, for all the characters. The Bayesian approach of ancestral character state reconstruction offers, however, a series of advantages over the single-tree approach or the ML model optimization on a Bayesian sample of trees because it does not involve restricting model parameters prior to reconstructing ancestral states, but rather allows a range of model parameters and ancestral character states to be sampled according to their posterior probabilities. From the distribution of the latter, conclusions on trait evolution can be made in a more satisfactorily way than when a substantial part of the uncertainty of the results is obscured by the focus on a single set of model parameters and associated ancestral states. The reconstructions of ancestral character states in Brachytheciastrum reveal rampant parallel morphological evolution. Most species previously described based on phenetic grounds are thus resolved of polyphyletic origin. Species polyphylly has been increasingly reported among mosses, raising severe reservations regarding current species definition.