Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns

Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns

Mosslummermönster : Systematik och historisk biogeografi hos Selaginellaceae

Selaginellaceae, spikemosses, is a heterosporous plant family belonging to the lycophytes. With an estimated age of some 350 million years, the family is historically important as one of the oldest known groups of vascular plants. Selaginellaceae is herbaceous with a worldwide distribution. However, the majority of the ca. 750 species in the single genus Selaginella are found in the tropics and subtropics. This thesis aims at elucidating the systematics and historical biogeography of Selaginellaceae. The evolutionary relationships of the family were inferred from DNA sequence data (plastid and single-copy nuclear) of one-third of the species richness in the group. Attention was paid to cover the previously undersampled taxonomic, morphological, and geographical diversity. Morphological features were studied and mapped onto the phylogeny. The results show an overall well-supported phylogeny and even more complex morphological patterns than previously reported. Despite this, many clades can be distinguished by unique suites of morphological features. With the phylogeny as a basis, together with the thorough morphological studies, a new subgeneric classification with seven subgenera, representing strongly supported monophyletic groups, is presented for Selaginella. By mainly using gross morphological features, easily studied by the naked eye or with a hand lens, the intention is that the classification should be useful to a broader audience. During the work with species determinations, it was revealed that the correct name for an endemic Madagascan Selaginella species is S. pectinata Spring, not S. polymorpha Badré as previously proposed. The robust phylogeny of Selaginellaceae allowed for a historical biogeographical analysis of the group. A time-calibrated phylogeny, together with extant species distribution data, formed the basis. The results show pre-Pangean diversification patterns, Gondwanan vicariance, and more recent Cenozoic long-distance dispersals. The many inferred transoceanic dispersals during the last 50 million years are surprising considering Selaginella’s large megaspores that are thought to have a negative effect on dispersal. In conclusion, this thesis presents a well-founded hypothesis of the evolutionary history of Selaginellaceae including its phylogeny, morphology, and historical biogeography. The thesis forms a firm basis for further studies on Selaginellaceae in particular, and gives us a better understanding of early land plant evolution in general

Selaginella_BI_con_MrBayes

The Bayesian tree (50% majority consensus) inferred from "Selaginella_alignment.nexus" using MrBayes. Figure 2 in article

A subgeneric classification of Selaginella (Selaginellaceae)

PREMISE OF THE STUDY: The lycophyte family Selaginellaceae includes approximately 750 herbaceous species worldwide, with the main species richness in the tropics and subtropics. We recently presented a phylogenetic analysis of Selaginellaceae based on DNA sequence data and, with the phylogeny as a framework, the study discussed the character evolution of the group focusing on gross morphology. Here we translate these findings into a new classification. METHODS: To present a robust and useful classification, we identified well-supported monophyletic groups from our previous phylogenetic analysis of 223 species, which together represent the diversity of the family with respect to morphology, taxonomy, and geographical distribution. Care was taken to choose groups with supporting morphology. KEY RESULTS: In this classification, we recognize a single genus Selaginella and seven subgenera: Selaginella, Rupestrae, Lepidophyllae, Gymnogynum, Exaltatae, Ericetorum, and Stachygynandrum. The subgenera are all well supported based on analysis of DNA sequence data and morphology. A key to the subgenera is presented. CONCLUSIONS: Our new classification is based on a well-founded hypothesis of the evolutionary relationships of Selaginella, and each subgenus can be identified by a suite of morphological features, most of them possible to study in the field. Our intention is that the classification will be useful not only to experts in the field, but also to a broader audience

Phylogeny of Selaginellaceae : There is value in morphology after all!

PREMISE OF THE STUDY: The cosmopolitan lycophyte family Selaginellaceae, dating back to the Late Devonian–Early Carboniferous, is notorious for its many species with a seemingly undifferentiated gross morphology. This morphological stasis has for a long time hampered our understanding of the evolutionary history of the single genus Selaginella. Here we present a large-scale phylogenetic analysis of Selaginella, and based on the resulting phylogeny, we discuss morphological evolution in the group. METHODS: We sampled about one-third of the approximately 750 recognized Selaginella species. Evolutionary relationships were inferred from both chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using a Bayesian inference approach. The morphology of the group was studied and important features mapped onto the phylogeny. KEY RESULTS: We present an overall well-supported phylogeny of Selaginella, and the phylogenetic positions of some previously problematic taxa (i.e., S. sinensis and allies) are now resolved with strong support. We show that even though the evolution of most morphological characters involves reversals and/or parallelisms, several characters are phylogenetically informative. Seven major clades are identified, which each can be uniquely diagnosed by a suite of morphological features. There is value in morphology after all! CONCLUSIONS: Our hypothesis of the evolutionary relationships of Selaginella is well founded based on DNA sequence data, as well as morphology, and is in line with previous findings. It will serve as a firm basis for further studies on Selaginella with respect to, e.g., the poorly known alpha taxonomy, as well as evolutionary questions such as historical biogeographic reconstructions

Data from: Phylogeny of Selaginellaceae: there is value in morphology after all!

PREMISE OF THE STUDY: The cosmopolitan lycophyte family Selaginellaceae, dating back to the Late Devonian–Early Carboniferous, is notorious for its many species with a seemingly undifferentiated gross morphology. This morphological stasis has for a long time hampered our understanding of the evolutionary history of the single genus Selaginella. Here we present a large-scale phylogenetic analysis of Selaginella, and based on the resulting phylogeny, we discuss morphological evolution in the group. METHODS: We sampled about one-third of the approximately 750 recognized Selaginella species. Evolutionary relationships were inferred from both chloroplast (rbcL) and single-copy nuclear gene data (pgiC and SQD1) using a Bayesian inference approach. The morphology of the group was studied and important features mapped onto the phylogeny. KEY RESULTS: We present an overall well-supported phylogeny of Selaginella, and the phylogenetic positions of some previously problematic taxa (i.e., S. sinensis and allies) are now resolved with strong support. We show that even though the evolution of most morphological characters involves reversals and/or parallelisms, several characters are phylogenetically informative. Seven major clades are identified, which each can be uniquely diagnosed by a suite of morphological features. There is value in morphology after all! CONCLUSIONS: Our hypothesis of the evolutionary relationships of Selaginella is well founded based on DNA sequence data, as well as morphology, and is in line with previous findings. It will serve as a firm basis for further studies on Selaginella with respect to, e.g., the poorly known alpha taxonomy, as well as evolutionary questions such as historical biogeographic reconstructions

Selaginella_alignment

Alignment of the combined three-region dataset (rbcL, pgiC, and SQD1). Sequences from "the sanguinolenta group" excluded. Data partitions and excluded characters are listed

Selaginella in Cretaceous amber from Myanmar

Selaginella (Selaginellales, Selaginellaceae) is the most speciose genus of lycophytes and, with approximately 750 recognized present-day species, also one of the largest genera of vascular plants. However, the evolutionary history of this species richness remains largely unresolved. Recent research suggests that Selaginella was diverse already in the mid-Cretaceous and shows that S. subg. Stachygynandrum dates back at least to the incipient Angiosperm Terrestrial Revolution some 100 million years ago. Here, we describe 20 new fossil-species of Selaginella based on fertile shoots and spores preserved in mid-Cretaceous Kachin amber from Myanmar and emend the previously described S. cretacea. Ten of the species (S. ciliifera, S. cretacea, S. grimaldii, S. heterosporangiata, S. longifimbriata, S. minutissima, S. ohlhoffiorum, S. patrickmuelleri, S. villosa, S. wangxinii) represent S. subg. Stachygynandrum because they possess anisophyllous strobili. The other eleven species have isophyllous strobili. Two of them (S. isophylla, S. wunderlichiana) are tentatively assigned to S. subg. Ericetorum, whereas the others (S. amplexicaulis, S. aurita, S. heinrichsii, S. konijnenburgiae, S. obscura, S. ovoidea, S. pellucida, S. tomescui, S. wangboi) cannot be placed into any fossil or extant subgenus. The fossils described in this study nearly duplicate the documented record of free-sporing plants from Kachin amber. The abundance and diversity of cryptogams, along with the absence of xerophytes among the taxa, is suggestive of constantly high humidity in the understory of the source forests of this amber.Peer reviewe

Did terrestrial diversification of amoebas (Amoebozoa) occur in synchrony with land plants?

Evolution of lineage diversification through time is an active area of research where much progress has been made in the last decade. Contrary to the situation in animals and plants little is known about how diversification rates have evolved in most major groups of protist. This is mainly due to uncertainty about phylogenetic relationships, scarcity of the protist fossil record and the unknown diversity within these lineages. We have analyzed the evolutionary history of the supergroup Amoebozoa over the last 1000 million years using molecular dating and species number estimates. After an origin in the marine environment we have dated the colonization of terrestrial habitats by three distinct lineages of Amoebozoa: Dictyostelia, Myxogastria and Arcellinida. The common ancestor of the two sister taxa, Dictyostelia and Myxogastria, appears to have existed before the colonization of land by plants. In contrast Arcellinida seems to have diversify in synchrony with land plant radiation, and more specifically with that of mosses. Detection of acceleration of diversification rates in Myxogastria and Arcellinida points to a co-evolution within the terrestrial habitats, where land plants and the amoebozoans may have interacted during the evolution of these new ecosystems