Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

https://doi.org/10.1016/j.ympev.2017.12.002Get rights and content

Highlights

  • The phylogeny of the Funariaceae is reconstructed based on 123 organellar genes.

  • This is the first moss phylogeny based on whole organellar exomes.

  • The monophyly of the genus Funaria is confirmed.

  • Most of the diversity was the result of a rapid diversification that occurred 28 mya.

  • The patterns of this diversification are comparable to those seen in angiosperms.

Abstract

Rapid diversifications of plants are primarily documented and studied in angiosperms, which are perceived as evolutionarily dynamic. Recent studies have, however, revealed that bryophytes have also undergone periods of rapid radiation. The speciose family Funariaceae, including the model taxon Physcomitrella patens, is one such lineage. Here, we infer relationships among major lineages within the Entosthodon-Physcomitrium complex from virtually complete organellar exomes (i.e., 123 genes) obtained through high throughput sequencing of genomic libraries enriched in these loci via targeted locus capture. Based on these extensive exonic data we (1) reconstructed a robust backbone topology of the Funariaceae, (2) confirmed the monophyly of Funaria and the polyphyly of Entosthodon, Physcomitrella, and Physcomitrium, and (3) argue for the occurrence of a rapid radiation within the Entosthodon-Physcomitrium complex that began 28 mya and gave rise more than half of the species diversity of the family. This diversification may have been triggered by a whole genome duplication and coincides with global Eocene cooling that continued through the Oligocene and Miocene. The Funariaceae join a growing list of bryophyte lineages whose history is marked by at least one burst of diversification, and our study thereby strengthens the view that bryophytes are evolutionarily dynamic lineages and that patterns and processes characterizing the evolution of angiosperms may be universal among land plants.

Introduction

Bryophytes (mosses, liverworts, and hornworts) differ significantly from other extant land plants by two plesiomorphic traits: a dominant gametophyte and an unbranched sporophyte that remains physically dependent on the maternal plant. Despite the rather simple architecture of their vegetative body (Goffinet and Buck, 2012), bryophytes are diverse, with as many as 20,000 extant species (Crosby et al., 1999, Söderström et al., 2016). Their position in the land plant tree of life (Cox et al., 2014, Wickett et al., 2014) and simple architecture (Schofield and Crum, 1972) may have led to their perception as primitive, “unmoved sphinxes from the past” (Crum, 1972). Furthermore, their rate of molecular evolution has been suggested as slower than in other plants (Stenøien, 2008), and broad disjunctions of conspecific populations assumed to result from vicariance were further interpreted as reflecting poor evolutionary potential (Frey et al., 1999). Although the view of bryophytes being sphinxes has generally been abandoned (e.g., Laenen et al. 2014), bryophytes continue to be labelled as primitive (e.g., Pedersen and Palmgren, 2017) and early (e.g., Liu et al. 2014) land plants, and to be implicitly perceived as slowly evolving.

This perception of bryophytes contrasts strongly with that of angiosperms, which are typically viewed as an evolutionarily dynamic lineage whose phylogenetic history is marked by episodically rapid diversifications (Givnish, 2010). Such rapid successions of divergences may be triggered by extrinsic or intrinsic events (Linder, 2008). They may follow dramatic shifts in selection resulting from climatic change or from novel ecological opportunities such as those provided by the rise of the Mediterranean climate meganiche (Guzmán et al., 2009, Linder, 2003) or following dispersal to young islands (Vitales et al., 2014). Increases in speciation rates may also follow large scale or whole genome duplication (WGD) resulting from autopolyploidy or allopolyploidy (Abbott et al., 2013, Pease et al., 2016, Soltis et al., 2016), which would broaden the templates for genetic, hence morphological, physiological or ontogenetic innovation (Rensing, 2014, Wang et al., 2012).

Despite the long held view of their evolutionary stasis, bryophytes are increasingly emerging as dynamic lineages with much of their diversity arising following successive bursts of diversification since the mid Mesozoic (Laenen et al., 2014). Some of these rapid radiations may be linked, for example, to the rise of angiosperm forests, which provided new habitats for epiphytes (Scheben et al., 2016, Silva et al., 2017), or may have been triggered by WGD, such as in Sphagnum (Devos et al., 2016, Shaw et al., 2016) and in the Hypnales (Shaw et al., 2003, Newton et al., 2007, Johnson et al., 2016b). Furthermore, broad geographic distributions resulting from rather recent (i.e., post Pangaea or Gondwana) events (e.g., Lewis et al., 2014) may be followed by allopatric speciation (e.g., Medina et al., 2012, Medina et al., 2013). These patterns and processes may account for much of the extant diversity of lineages of mosses, such as the Funariaceae. This family likely incurred one or more past WGD in its history (Rensing et al., 2007), is globally distributed, and holds many narrow endemics (Fife, 1982).

The Funariaceae have long provided model taxa for developmental (e.g. Wettstein, 1925, French and Paolillo, 1975) and, more recently, genomic and evo-devo studies (Lang et al., 2016). The family arose early in the diversification of mosses with arthrodontous peristomes (Cox et al., 2014, Cox et al., 2004) and comprises now approximately 255 species (Crosby et al., 1999). Its history is marked by a first split segregating the Funarioideae and Pyramiduloideae (Werner et al., 2007), followed by the split between Funaria and the rapidly diversifying Entosthodon-Physcomitrium (E-P) clade (Liu et al., 2012). The latter comprises a large assemblage of species exhibiting a broad range of sporophyte morphologies likely resulting from recurrent reduction, as best exemplified by the polyphyly of the genus Physcomitrella (Liu et al., 2012). The potentially extensive homoplasy in these traits called for inferences from alternative characters. Variation in ten loci sampled from all three genome compartments proved, however, insufficient to robustly resolve the relationships among lineages within the E-P clade (Liu et al. 2012).

Here we seek to further strengthen the reconstruction of the evolutionary history of the Funariaceae, resolve the radiation within the Funarioideae and provide a time frame for their diversification. We sampled all organellar exons via liquid phase bait-mediated hybridization and sequenced 91 multiplexed enriched libraries, allowing for a cost-effective sampling of extensive loci across taxa, and resulting in near maximum coverage and significant depth, compared to retrieving organellar loci from randomly sequenced genomic libraries (e.g. Liu et al., 2014, Shaw et al., 2016). We compiled genome-scale data for 78 Funariaceae and 13 outgroup samples via high-throughput sequencing of genomic libraries enriched in all coding genes of the plastid and mitochondrial genomes. The exonic dataset should overcome the limitations of the ten organellar and nuclear loci targeted by Liu et al. (2012), considering that the organellar exomes contain a rich phylogenetic signal in the Funariaceae (Liu et al., 2013). The alignment of plastid and mitochondrial protein coding genes should be relatively unambiguous due to codon homology and absence of paralogy, given that the mitochondrial and plastid genomes seem to be maternally inherited in bryophytes (Jankowiak et al., 2005, Natcheva and Cronberg, 2007). Since meiosis is monoplastidic (Brown and Lemmon, 2016), no regular recombination occurs during the life cycle, hence phylogenetic inference from (at least) the plastid data should not be affected by other, more complex, phenomena such as hybridization and incomplete lineage sorting. This approach, however, is a tradeoff, since it offers only partial insight (i.e., maternal) into, for example, the affinities of allopolyploids. Nevertheless, these extensive exonic data provide a robust dataset for a) reconstructing the backbone topology of the Funariaceae, b) testing the monophyly of major genera within the Funariaceae, and c) assessing timing of diversification of the E-P clade.

Section snippets

Material and methods

We sampled 78 specimens from the Funariaceae, employing their closest relatives as outgroups up to a total of 91 samples (Table 1). To assess the reliability of the methodology for library preparation and sequencing error, some specimens were represented by two samples (Chamaebryum pottioides; Discelium nudum; Entosthodon obtusus and Physcomitrium eurystomum). Since wild populations of Funariaceae develop gametophytes in small clumps, typically insufficient for genomic extraction, moss samples

Results and discussion

Sequencing multiplexed enriched genomic libraries yielded 96% of all the plastid protein coding sequences for the 91 samples (average coverage 95.4%, standard deviation 20%). All the sequences of the mitochondrial exons were recovered except a fragment of the atp9 gene (total chondrome average coverage is 99%, with a standard deviation of 7%). The average pairwise distance among Funarioideae for the whole plastid exome is 4.3% (3.2% StDev), and for the mitochondrial exome 0.9% (1.3% StDev). The

Acknowledgements

This study was made possible through financial support from the US National Science Foundation (grants DEB-1146295, DEB-1354631, and DEB-1240045 to Goffinet; DEB-1239992 and DEB-1342873 to Wickett) as well as the National Natural Science Foundation of China for Liu (grant 31470314). The National Research Foundation of South Africa, the University of Cape Town Research Committee, and the Agence Nationale de La Recherche, Conseil Régional de La Réunion, Conseil Régional de Guadeloupe, Government

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