A phylogenetic analysis of monocotyledons based on the chloroplast gene rps4, using parsimony and a new numerical phenetics method

Studies of Vietnamese Pteridophyte Flora 3

This is the third paper in a series dedicated to updating the knowledge of the Vietnamese pteridophyte flora. Based on recent collections, we first reported three new national records of ferns: Haplopterisyakushimensis, Lindsaeakohkongensis, and Pterispseudowulaiensis. Secondly, we conducted phylogenetic analyses to investigate the placements of Lindsaeakohkongensis and Leptochiluspoilanei, each based on three plastid DNA markers. Our results revealed that Lindsaeakohkongensis is sister to L.ensifolia, while Leptochiluspoilanei is embedded within L.cantoniensis. We discussed these results in the context of systematics. Lastly, we reported chromosome numbers for 20 fern species in Vietnam. For seven of these species, including Gymnosphaerasalletii, Lepisorusspicatus, Leptochiluspoilanei, Pteridryscostularis, Pterislatipinna, Pyrrosiaeberhardtii, and Tectariasetulosa, these counts were recorded for the first time. Additionally, three new cytotypes were identified for Diplaziumdoederleinii, Pterisesquirolii, and Tectariaharlandii. This study underscores the need for more diverse data, including DNA sequences, chromosome numbers, and reproductive modes, to be collected and integrated into systematic studies and taxonomic treatments to enhance our understanding of Vietnam's pteridophyte flora.

Multiple colonization and dispersal events hide the early origin and induce a lack of genetic structure of the moss Bryum argenteum in Antarctica

The dispersal routes of taxa with transoceanic disjunctions remain poorly understood, with the potential roles of Antarctica not yet demonstrated. Mosses are suitable organisms to test direct intra-Antarctic dispersal, as major component of the extant Antarctic flora, with the cosmopolitan moss Bryum argenteum as ideal target species. We analyzed the genetic structure of B. argenteum to provide an evolutionary time frame for its radiation and shed light into its historical biogeography in the Antarctic region. We tested two alternative scenarios: (a) intra-Antarctic panmixia and (b) intra-Antarctic genetic differentiation. Furthermore, we tested for evidence of the existence of specific intra-Antarctic dispersal routes. Sixty-seven new samples (40 collected in Antarctica) were sequenced for ITS nrDNA and rps4 cpDNA regions, and phylogenetic trees of B. argenteum were constructed, with a focus on its Southern Hemisphere. Combining our new nrDNA dataset with previously published datasets, we estimated time-calibrated phylogenies based on two different substitution rates (derived from angiosperms and bryophytes) along with ancestral area estimations. Minimum spanning network and pairwise genetic distances were also calculated. B. argenteum was potentially distributed across Africa and Antarctica soon after its origin. Its earliest intra-Antarctic dispersal and diversification occurred during a warming period in the Pliocene. On the same timescale, a radiation took place involving a dispersal event from Antarctica to the sub-Antarctic islands. A more recent event of dispersal and diversification within Antarctica occurred during a warm period in the Pleistocene, creating favorable conditions also for its colonization outside the Antarctic continent worldwide. We provide evidence supporting the hypothesis that contemporary populations of B. argenteum in Antarctica integrate a history of both multiple long-range dispersal events and local persistence combined with in situ diversification. Our data support the hypothesis that B. argenteum has been characterized by strong connectivity within Antarctica, suggesting the existence of intra-Antarctic dispersal routes.

Phylogeny, historical biogeography and characters evolution of the drought resistant fern Pyrrosia Mirbel (Polypodiaceae) inferred from plastid and nuclear markers

Pyrrosia s.l. comprises ca. 60 species with a disjunct Africa/Asia and Australia distribution. The infrageneric classification of Pyrrosia s.l. is controversial based on the phylogenetic analyses of chloroplast markers and morphology. Based on the expanded taxon sampling of Pyrrosia s.l. (51 species), we investigated its phylogeny, biogeography, character evolution and environmental adaptation by employing five chloroplastid markers (rbcL, matK, psbA-trnH, and rps4 + rps4-trnS) and one single (low)-copy nuclear gene, LEAFY. Pyrrosia s.l. was divided into six major clades and eight subclades. Reticulate evolution was revealed both among clades and among species in Pyrrosia s.l. Ancestral character state optimization revealed high levels of homoplastic evolution of the diagnostic characters in Pyrrosia s.l., while the crassulacean acid metabolism pathway seems to have an independent origin. Molecular dating and biogeographic diversification analyses suggested that Pyrrosia s.l. originated no later than the Oligocene and the main clades diversified during the Oligocene and Miocene, with southern Asia, the Indo-China Peninsula and southwestern and southern China as the most likely ancestral areas. Transoceanic long-distance dispersal, rather than vicariance, contributed to the intercontinental disjunction. Diversification scenarios of Pyrrosia s.l. under geological movements and climate fluctuation are also discussed.

Adetogramma (Polypodiaceae), a new monotypic fern genus segregated from Polypodium

Polypodiaceae is one of the most diverse and abundant families of ferns in tropical and subtropical forests. Despite multiple studies investigating its phylogeny and taxonomy, several generic boundaries within the family still need clarification. One of the most problematic circumscriptions is that of Polypodium L., and one species that still contributes to this uncertainty is Polypodium chrysolepis Hook. The main goal of this study was to use molecular and morphological data to clarify the relationships of P. chrysolepis inside the polygrammoid clade. Sequences from three plastid regions (cpDNA - rbcL, rps4 and rps4-trnS IGS) from fifty species belonging to thirty-two genera of Polypodiaceae were analyzed using maximum likelihood and Bayesian inference. Polypodium chrysolepis constitutes an isolated lineage among the neotropical polygrammoid ferns, close to Serpocaulon and the grammitids, and is recognized here in a new genus. It can be distinguished by its entire leaves with free veins and peltate, pedicellate, lanceolate paraphyses. A new combination, Adetogramma chrysolepis, is proposed and a new taxonomic treatment is presented; its conservation status was assessed using IUCN Red List Categories and Criteria.

Phylogenetic analyses place the monotypic Dryopolystichum within Lomariopsidaceae

The monotypic fern genus Dryopolystichum Copel. combines a unique assortment of characters that obscures its relationship to other ferns. Its thin-walled sporangium with a vertical and interrupted annulus, round sorus with peltate indusium, and petiole with several vascular bundles place it in suborder Polypodiineae, but more precise placement has eluded previous authors. Here we investigate its phylogenetic position using three plastid DNA markers, rbcL, rps4-trnS, and trnL-F, and a broad sampling of Polypodiineae. We also provide new data on Dryopolystichum including spore number counts, reproductive mode, spore SEM images, and chromosome counts. Our maximum-likelihood and Bayesian-inference phylogenetic analyses unambiguously place Dryopolystichum within Lomariopsidaceae, a position not previously suggested. Dryopolystichum was resolved as sister to a clade comprising Dracoglossum and Lomariopsis, with Cyclopeltis as sister to these, but clade support is not robust. All examined sporangia of Dryopolystichum produced 32 spores, and the chromosome number of sporophyte somatic cells is ca. 164. Flow cytometric results indicated that the genome size in the spore nuclei is approximately half the size of those from sporophyte leaf tissues, suggesting that Dryopolystichum reproduces sexually. Our findings render Lomariopsidaceae as one of the most morphologically heterogeneous fern families. A recircumscription is provided for both Lomariopsidaceae and Dryopolystichum, and selected characters are briefly discussed considering the newly generated data.

Novel biogenic aggregation of moss gemmae on a disappearing African glacier

Tropical regions are not well represented in glacier biology, yet many tropical glaciers are under threat of disappearance due to climate change. Here we report a novel biogenic aggregation at the terminus of a glacier in the Rwenzori Mountains, Uganda. The material was formed by uniseriate protonemal moss gemmae and protonema. Molecular analysis of five genetic markers determined the taxon as Ceratodon purpureus, a cosmopolitan species that is widespread in tropical to polar region. Given optimal growing temperatures of isolate is 20-30 °C, the cold glacier surface might seem unsuitable for this species. However, the cluster of protonema growth reached approximately 10 °C in daytime, suggesting that diurnal increase in temperature may contribute to the moss's ability to inhabit the glacier surface. The aggregation is also a habitat for microorganisms, and the disappearance of this glacier will lead to the loss of this unique ecosystem.

Elevational patterns of genetic variation in the cosmopolitan moss Bryum argenteum (Bryaceae)

PREMISE OF THE STUDY

The Baas Becking tenet posits that 'everything is everywhere, but the environment selects' to explain cosmopolitan distributions in highly vagile taxa. Bryophyte species show wider distributions than vascular plants and include examples of truly cosmopolitan ranges, which have been interpreted as a result of high dispersal capacities and ecological plasticity. In the current study, we documented patterns of genetic structure and diversity in the cosmopolitan moss Bryum argenteum along an elevational gradient to determine if genetic diversity and structure is homogenized by intense migrations in the lack of ecological differentiation. •

METHODS

60 specimens were collected in the Sierra Nevada Mountains (Spain) between 100 and 2870 m and sequenced for ITS and rps4. Comparative analyses, genetic diversity estimators, and Mantel's tests were employed to determine the relationship between genetic variation, elevation, and geographic distance and to look for signs of demographic shifts. •

KEY RESULTS

Genetic diversity peaked above 1900 m and no signs of demographic shifts were detected at any elevation. There was a strong phylogenetic component in elevational variation. Genetic variation was significantly correlated with elevation, but not with geographic distance. •

CONCLUSIONS

The results point to the long-term persistence of Bryum argenteum in a range that was glaciated during the Late Pleistocene. Evidence for an environmentally driven pattern of genetic differentiation suggests adaptive divergence. This supports the Baas Becking tenet and indicates that ecological specialization might play a key role in explaining patterns of genetic structure in cosmopolitan mosses.

Phylogeny of the Asparagales based on three plastid and two mitochondrial genes

PREMISE OF THE STUDY

The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial.

METHODS

Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated.

KEY RESULTS

The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent.

CONCLUSIONS

Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.

Phylogeography of the Sino-Himalayan fern Lepisorus clathratus on "the roof of the world"

BACKGROUND

The Qinghai-Tibetan Plateau (QTP) and its southern and southeastern mountain ranges, Himalaya-Hengduan Mountains (HHM), are one of the most extensive habitats for alpine plants in the world. How ferns occurring in QTP and HHM changed their distribution ranges in response to Quaternary climatic oscillations remains almost unknown.

METHODOLOGY AND RESULTS

We employed sequences of two chloroplast DNA regions, rps4-trnS and trnL-trnF, to reconstruct phylogeography of the Sino-Himalayan fern Lepisorus clathratus, occurring mainly in the QTP and HHM. Individuals of this species have either dehiscent or indehiscent sporangia with the latter evolved from the plesiomorphic dehiscent forms. Based on a range-wide sampling, we detected 27 cpDNA haplotypes that were divided into five groups by network analyses. Populations in the Hengduan Mountains possess the highest genetic diversity, while a single haplogroup is detected across the north-central region. A distinct phylogeographical subdivision was detected between the Hengduan Mountains and north-central region by AMOVA analysis. The haplogroup distribution pattern, coalescence and AMOVA analysis suggest that a long term survival area (refugia) of the species was located in the Hengduan Mountains during glaciations, with probable range expansions into north-central regions during interglacial periods. Populations with indehiscent sporangium can carry private haplotypes and are inclined to maintain genetic homogeneity. One group with indehiscent sporangia most likely survived in situ on the QTP during glaciations.

CONCLUSIONS/SIGNIFICANCE

This study for the first time sheds light on the response of alpine ferns in the QTP and HHM to the Quaternary climatic oscillations.

Unraveling the phylogeny of polygrammoid ferns (Polypodiaceae and Grammitidaceae): exploring aspects of the diversification of epiphytic plants

We explore the phylogeny of the polygrammoid ferns using nucleotide sequences derived from three plastid loci for each of 98 selected species. Our analyses recovered four major monophyletic lineages: the loxogrammoids, two clades consisting of taxa restricted to the Old World, and a largely neotropical clade that also includes the pantropical Grammitidaceae. The loxogrammoid lineage diverges first and is sister to a large clade comprising the three remaining species-rich lineages. One paleotropical clade includes the drynarioid and selligueoid ferns, whereas the second paleotropical clade includes the platycerioids, lepisoroids, microsoroids, and their relatives. The grammitids nest within the neotropical clade, although the sister taxon of this circum-tropic, epiphytic group remains ambiguous. Microsorum and Polypodium, as traditionally defined, were recovered as polyphyletic. The relatively short branch lengths of the deepest clades contrast with the long branch lengths leading to the terminal groups. This suggests that the polygrammoid ferns arose through an old, rapid radiation. Our analysis also reveals that the rate of substitution in the grammitids is remarkably higher relative to other polygrammoids. Disparities in substitution rate may be correlated with one or more features characterizing grammitids, including species richness, chlorophyllous spores, and an extended gametophytic phase.

18S gene trees are positively misleading for monocot/dicot phylogenetics

Monocots are consistently paraphyletic in 18S gene trees in all studies to date. This anomaly is generally expressed in the phylogenetic associations of two lineages, that of Acoraceae, which is excluded from the monocots, and Ceratophyllaceae, which sometimes clusters within the monocots. Six explanations for these unexpected results are proposed: (1) erroneous published sequences, (2) actual paraphyly of monocots with dicots, (3) insufficient taxon density among relevant taxa; (4) long-branch attraction between selected taxa, (5) an anomalous 18S paralogue in the basal species of monocots, and (6) differential lineage sorting or other molecular evolutionary events. Tests of each of these hypotheses were conducted. For the first five hypotheses, test results refuted the hypothesis. Support for the sixth hypothesis, differential lineage sorting, is the strongest. Since lineage sorting seems to be restricted to a few species, identification and removal of these species prior to performing separate or combined phylogenetic analysis of DNA data incorporating sequences from 18S may be advisable.

Floral structure and development of Acoraceae and its systematic relationships with basal angiosperms

Flower development and anatomy of Acorus calamus and flower anatomy of A. gramineus were studied. Findings were compared with published reports on paleoherbs. Important developmental features include an abaxially median tepal that is initiated first and is similar to a flower-subtending bract and unidirectional flower development with an inversion of organ initiation sequence in the second tepal whorl. The mature gynoecium is largely synascidiate, but early development of carpels is plicate, and the apocarpous portion persists up to anthesis. The carpels form dorsal bulges on the style, enclosing longitudinal intercarpellary slits. The dominance of the synascidiate portion and the apical position of the placenta result from a late and distinct basal elongation of the gynoecium. Stigma, pollen transmitting tract, and ovary are filled with secretion. Secretory papillae are present from the stigma to the placenta; papillae also occur on the rims of the integuments of the ovules. In the uppermost part of the inflorescence, the adaxial floral sectors are reduced in number and structure, and at the apex of the inflorescence, a peloria-like structure is formed. Developmental and morphological similarities seem to be closer between Acorus and Piperales than between Acorus and other magnoliids.