Phylogeography and colonization pattern of subendemic round-leaved oxeye daisy from the Dinarides to the Carpathians.

The Carpathians are an important biodiversity hotspot and a link between mountain ranges on the European continent. This study investigated the phylogeography of one the Carpathian subendemics, Leucanthemum rotundifolium, which is distributed throughout the range and in one isolated population outside it. Range-wide sampling was used to examine phylogeographic patterns by sequencing uniparentally inherited chloroplast markers that exemplify seed dispersal. Reconstruct Ancestral State in Phylogenies (RASP) software, Bayesian binary Markov Chain Monte Carlo (BBM) analysis, and ecological niche modeling based on concatenated results of five algorithms were used to infer migration routes and examine links with other species through phylogeny. The round-leaved oxeye daisy is an example of organisms that reached the Carpathians through a southern "Dacian" migration route, most probably through long-distance dispersal. Dating placed the events in the Pleistocene and supported migrations during cooler periods and stasis/isolation followed by separation in the interglacials. Haplotype diversification indicated that after L. rotundifolium reached the area around the Fagaras Mountains, several migration events occurred leading to colonization of the Southern Carpathians followed by migration to the Apuseni Mountains, the Eastern Carpathians, and finally the Western Carpathians. The results are consistent with previous phylogeographic studies in this region and indicate several novel patterns.

Niche conservatism and evolution of climatic tolerance in the Neotropical orchid genera Sobralia and Brasolia (Orchidaceae).

Sobralia and Brasolia form a large complex of Neotropical Orchidaceae. Although the molecular and morphological studies allowed to increase the rate of work on the modern classification of the taxa, they still require the attention as remaining without complete revision. The niche similarity analysis between representatives of Sobralia and recently segregated from this taxon-genus Brasolia is presented. The ecological tolerance evolution within the group was investigated with molecular clock analysis and phylogeny as the background. The phylogenetic analysis has confirmed the previous results and placed Brasolia representatives in a single clade with Elleanthus and Sobralia core as a separated group. The molecular clock analysis suggests that Sobralia and Brasolia are relatively young groups that evolved between 8.5 and 8 million years ago. Distribution of suitable niches of studied species is generally congruent with the known geographical ranges of particular taxa. The calculated niche overlap did not indicate any correlation between niche overlap and species phylogenetic relationships and remains low for both intra- and intergeneric relationships. The reconstruction of climatic tolerance evolution indicated that the studied species of Brasolia and Sobralia are characterized by generally similar ecological tolerance for most of the analyzed variables.

An overlooked dispersal route of Cardueae (Asteraceae) from the Mediterranean to East Asia revealed by phylogenomic and biogeographical analyses of Atractylodes.

BACKGROUND AND AIMS: The East Asian-Tethyan disjunction pattern and its mechanisms of formation have long been of interest to researchers. Here, we studied the biogeographical history of Asteraceae tribe Cardueae, with a particular focus on the temperate East Asian genus Atractylodes DC., to understand the role of tectonic and climatic events in driving the diversification and disjunctions of the genus. METHODS: A total of 76 samples of Atractylodes from 36 locations were collected for RAD-sequencing. Three single nucleotide polymorphism (SNP) datasets based on different filtering strategies were used for phylogenetic analyses. Molecular dating and ancestral distribution reconstruction were performed using both chloroplast DNA sequences (127 Cardueae samples) and SNP (36 Atractylodes samples) datasets. KEY RESULTS: Six species of Atractylodes were well resolved as individually monophyletic, although some introgression was identified among accessions of A. chinensis, A. lancea and A. koreana. Dispersal of the subtribe Carlininae from the Mediterranean to East Asia occurred after divergence between Atractylodes and Carlina L. + Atractylis L. + Thevenotia DC. at ~31.57 Ma, resulting in an East Asian-Tethyan disjunction. Diversification of Atractylodes in East Asia mainly occurred from the Late Miocene to the Early Pleistocene. CONCLUSIONS: Aridification of Asia and the closure of the Turgai Strait in the Late Oligocene promoted the dispersal of Cardueae from the Mediterranean to East China. Subsequent uplift of the Qinghai-Tibet Plateau as well as changes in Asian monsoon systems resulted in an East Asian-Tethyan disjunction between Atractylodes and Carlina + Atractylis + Thevenotia. In addition, Late Miocene to Quaternary climates and sea level fluctuations played major roles in the diversification of Atractylodes. Through this study of different taxonomic levels using genomic data, we have revealed an overlooked dispersal route between the Mediterranean and far East Asia (Japan/Korea) via Central Asia and East China.

Chrysanthemumdabieshanense, a new name for Chrysanthemumvestitum var. latifolium (Asteraceae, Anthemideae).

Recent phylogenetic analyses have revealed that Chrysanthemumvestitumvar.latifolium and C.vestitumvar.vestitum were placed in different clades based on their chloroplast genomes and nuclear LFAFY gene sequences. Accordingly, based on previous morphological analysis, molecular phylogenetic results, fieldwork, and herbarium studies, Chrysanthemumvestitumvar.latifolium should be raised to the species level. Considering the condition of the material found and Articles 6.9, 6.11, 41.2, 58.1 of the International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code) that is currently in force, Chrysanthemumdabieshanense Z.X.Fu, A.G.Zhen, & Y.P.Ma, nom. nov. is proposed as the new name for Chrysanthemumvestitumvar.latifolium J.Zhou & Jun Y.Chen. The detailed emended description, distribution map, insights into its habitat, and an updated comparative morphological study are presented in this study.

Development of nuclear and chloroplast polymorphic microsatellites for Crossostephium chinense (Asteraceae).

BACKGROUND: Crossostephium chinense is a traditional Chinese medicinal herb and it is often cultivated as an ornamental plant. Previous studies on this species mainly focused on its chemical composition and it was rarely represented in genetic studies, and thus genomic resources remain scarce. METHODS AND RESULTS: Both chloroplast and nuclear polymorphic microsatellites of C. chinense were screened from genome skimming data of two individuals. 64 and 63 cpSSR markers were identified from two chloroplast genomes of C. chinense. A total of 133 polymorphic nSSRs were developed. Ten nSSRs were randomly selected to test their transferability across 35 individuals from three populations of C. chinense, and 20 individuals each of Artemisia stolonifera and A. argyi. Cross-amplifications were successfully done for C. chinense and were partially amplified for both Artemisia species. The number of alleles varied from two to nine. The observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 0.286 and from 0.029 to 0.755, respectively. CONCLUSIONS: In this study, we developed polymorphic cpSSRs and nSSRs markers for C. chinense based on genome skimming sequencing. These genomic resources will be valuable for population genetics and conservation studies in C. chinense and Artemisia.

The impact of global warming on the niches and pollinator availability of sexually deceptive orchid with a single pollen vector.

Orchidaceae are among the most endangered plants in the world. Considering the sensitive nature of pollinator-plant relationship the most vulnerable are species which are dependent on a single pollen vector. In this paper the future distribution of suitable niches of Australian sexually deceptive orchid Leporella fimbriata and its pollinator (Myrmecia urens) was estimated using three machine learning algorithms. While the potential range of fringed hare orchid depending on modelling method will be larger or slightly reduced than currently observed, the ant will face significant loss of suitable niches. As a result of global warming the overlap of orchid and its only pollen vector will most probably decrease. The unavailability of pollen vector will lead to decreased reproductive success and as a result it will be a great threat for L. fimbriata existence.

Evaluation metrics and validation of presence-only species distribution models based on distributional maps with varying coverage.

We examine how different datasets, including georeferenced hardcopy maps of different extents and georeferenced herbarium specimens (spanning the range from 100 to 85,000 km2) influence ecological niche modeling. We check 13 of the available environmental niche modeling algorithms, using 30 metrics to score their validity and evaluate which are useful for the selection of the best model. The validation is made using an independent dataset comprised of presences and absences collected in a range-wide field survey of Carpathian endemic plant Leucanthemum rotundifolium (Compositae). Our analysis of models' predictive performances indicates that almost all datasets may be used for the construction of a species distributional range. Both very local and very general datasets can produce useful predictions, which may be more detailed than the original ranges. Results also highlight the possibility of using the data from manually georeferenced archival sources in reconstructions aimed at establishing species' ecological niches. We discuss possible applications of those data and associated problems. For the evaluation of models, we suggest employing AUC, MAE, and Bias. We show an example of how AUC and MAE may be combined to select the model with the best performance.

On the Leucanthemopsis alpina (L.) Heywood growing in the Illyrian region.

Leucanthemopsis alpina (L.) Heywood (Asteraceae, Anthemideae) is a small, caespitose plant growing in high alpine environments in all the main southern European mountain ranges. However, the species status in the Balkan Peninsula (and especially in the Dinaric Alps) is not very well known. Surrounding this area, different L. alpina subspecies are found in the Eastern Alps and in the Carpathians. These subspecies differ from one another, both morphologically and in chromosome number. The present study aims to better characterise the populations of L. alpina in the Illyrian and Balkan regions by undertaking a comprehensive survey of herbarium collections for the species in this area, by applying flow cytometry for ploidy determination and by sequencing of two chloroplast markers. Results from our investigation suggest that the only population of the species in the Dinaric Alps is found in the Vranica Mts (Bosnia and Herzegovina). This population consists of diploid plants (unlike tetraploid populations from the Eastern Alps) that are slightly distinct genetically from those of the subspecies growing in the Eastern Alps and the Tatra Mts. Both the ploidy and their genetic distinction indicate that Vranica Mts most probably served as a refugium for the species during the Pleistocene glaciations. Considering its isolated geographical range and its genetic distinction, the population of L. alpina growing in the Vranica Mts should be considered as a separate subspecies.

Climatic niche shift and possible future spread of the invasive South African Orchid Disa bracteata in Australia and adjacent areas.

Orchids are generally regarded as plants with an insignificant invasive potential and so far only one species has proved to be harmful for native flora. However, previous studies on Epipactis helleborine and Arundina graminifolia indicate that the ecological aspects of range extension in their non-native geographical range are not the same for all species of orchids. Disa bracteata in its native range, South Africa, is categorized as of little concern in terms of conservation whereas in Australia it is naturalized and considered to be an environmental weed. The aim of this research was to determine the ecological preferences enabling the spread of Disa bracteata in Western and South Australia, Victoria and Tasmania and to evaluate the effect of future climate change on its potential range. The ecological niche modeling approach indicates that most of the accessible areas are already occupied by this species but future expansion will continue based on four climate change scenarios (rcp26, rcp45, rcp60, rcp85). Further expansion is predicted especially in eastern Australia and eastern Tasmania. Moreover, there are some unpopulated but suitable habitats in New Zealand, which according to climate change scenarios will become even more suitable in the future. The most striking result of this study is the significant difference between the environmental conditions recorded in the areas which D. bracteata naturally inhabits and invasive sites-that indicates a possible niche shift. In Australia the studied species continues to populate a new niche or exploit habitats that are only moderately represented in South Africa.

Climatic niche of Selinum alatum (Apiaceae, Selineae), a new invasive plant species in Central Europe and its alterations according to the climate change scenarios: Are the European mountains threatened by invasion?

In recent years, a few established populations of Selinum alatum have been found in the Eastern Carpathians outside its native range that is the Caucasus and the Armenian Highlands. The species is spreading predominantly in Poland where it can outcompete native plants in certain cases. This study addresses a potential climatic niche of the plant with the special aims to illuminate future spreading and indicate areas suitable for invasion. Our results show that the extent of the favourable habitat of the species is broader than currently known. This suggests that the plant has the ability to become a potential new element in some semi-natural or disturbed ecosystems associated with mountainous areas, especially in Central and Southern Europe. Future (2070) models mostly rendered similar suitability maps, but showed slight differences over particular areas and a contraction of suitable habitats, mainly in the northern part of the non-native range.

Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives.

In the present study we investigate the concept of phylogenetic niche conservatism (PNC) within the American species of angraecoid orchids (Campylocentrum and Dendrophylax) and their closest relatives in the Old World (Angraecum) using ecological niche modelling (ENM). The predicted niche occupancy profiles were matched with the outcomes of previous phylogenetic studies to reconstruct the evolution of climatic suitability within the orchid group studied and evaluate the role of niche differentiation in the speciation of Angraecinae. No correlation between preferred niches and taxonomic relationships within the orchid group studied was revealed. The climatic suitability of the majority of the species overlapped each other, either fully or partially. This pattern is also present in the species of other orchid genera. Our research confirms a significant level of PNC in Orchidaceae, even within taxa exhibiting a transatlantic disjunction. The analysis of the evolution of climatic suitability indicated that the adaptation to various climatic conditions is not a factor that has driven speciation within orchids studied.

Evolution of the climatic tolerance and postglacial range changes of the most primitive orchids (Apostasioideae) within Sundaland, Wallacea and Sahul.

The location of possible glacial refugia of six Apostasioideae representatives is estimated based on ecological niche modeling analysis. The distribution of their suitable niches during the last glacial maximum (LGM) is compared with their current potential and documented geographical ranges. The climatic factors limiting the studied species occurrences are evaluated and the niche overlap between the studied orchids is assessed and discussed. The predicted niche occupancy profiles and reconstruction of ancestral climatic tolerances suggest high level of phylogenetic niche conservatism within Apostasioideae.

Detecting reticulate relationships among diploid Leucanthemum Mill. (Compositae, Anthemideae) taxa using multilocus species tree reconstruction methods and AFLP fingerprinting.

We examined the evolutionary history of the diploid representatives of the genus Leucanthemum Mill. (Compositae, Anthemideae), which constitutes an extensive polyploid complex comprising around 41 species with ploidy levels ranging from 2x to 22x. The inference of phylogenetic relationships even on the diploid level is complicated in this genus due to the overlay of hybridisation and incomplete lineage sorting processes leading to incongruence among gene trees based on nuclear and plastid sequence information. Species tree and network reconstructions were based on gene trees from nine low-copy nuclear markers and the concatenated sequence information for five intergenic spacer regions of the chloroplast genome, either sequenced by Roche 454 pyrosequencing techniques or traditional Sanger sequencing techniques. Additional phylogenetic information came from multi-locus AFLP-fingerprinting of representative individuals of all diploid taxa under study and the subsequent analysis of AFLP patterns with Bayesian clustering and network reconstruction methods. To distinguish between hybridisation and incomplete lineage sorting, we developed and utilized a new 'hybrid index' calculation for individual taxa of the data set, which was compared to a simulated null-distribution assuming the occurrence of incomplete lineage sorting alone for pinpointing taxa with a significant hybrid signal. As a result, two species groups with contrasting patterns of gene flow and/or hybrid speciation signals could be identified in the diploids of Leucanthemum: (a) an early-diverging stock of allopatrically distributed diploid species with a lack of evidence for recent hybridisation events among its members and (b) a more recently radiated taxon assemblage with morphologically less clearly circumscribed taxa and a pronounced signal of gene flow among lineages and several candidate taxa, for which a homoploid hybrid origin may be considered.

The reticulate evolutionary history of the polyploid NW Iberian Leucanthemum pluriflorum clan (Compositae, Anthemideae) as inferred from nrDNA ETS sequence diversity and eco-climatological niche-modelling.

The genus Leucanthemum Mill. is a species-rich polyploid complex of southern and central Europe, comprising 41 species with ploidy levels ranging from 2x to 22x. The Leucanthemum pluriflorum clan, a geographically isolated species group of the NW Iberian Peninsula, comprises the diploid L. pluriflorum, the tetraploids Leucanthemumircutianum subsp. pseudosylvaticum and Leucanthemum×corunnense (being a putative hybrid taxon based on a cross between L. pluriflorum and Leucanthemummerinoi), and the two hexaploids Leucanthemumsylvaticum and L. merinoi. In order to reconstruct the evolutionary history of this species group, we analysed sequence variation at the external transcribed spacer region of the nuclear ribosomal repeat (nrDNA ETS) for its members and for a number of other diploid species of Leucanthemum. Our results indicate that there are two major ETS ribotypes present in Leucanthemum, with some of the diploid species fixed for either of the two types and several species (among them L. pluriflorum) exhibiting both types. This polymorphism at the nrDNA ETS locus suggests either gene flow among some of the diploid species (possibly via polyploids) or a homoploid hybrid origin of some of those diploids. Additionally, patterns of ETS ribotype sharing among populations of the four species of the L. pluriflorum clan suggest that the tetraploid L. ircutianum subsp. pseudosylvaticum and the hexaploids L. sylvaticum and L. merinoi have an allopolyploid origin with L. pluriflorum as the maternal parent. Eco-climatological modelling of present and past (last glacial maximum, LGM) distribution areas of the members of the L. pluriflorum clan indicates that the diploid L. pluriflorum may have undergone geographical differentiation into northern (Galician) and southern (central Portuguese) coastal lineages that could account for the two chloroplast haplotype groups observable in the tetra- and hexaploids. Later climatic changes in the Holocene could then have led to the extinction of southern diploid lineages. A distinct overlap of present and past (LGM) potential distribution ranges of L. pluriflorum with those of the N Iberian endemics Leucanthemumgallaecicum and Leucanthemumgaudinii subsp. cantabricum may indicate that one of the latter species may have acted as the paternal parent in the formation of the polyploids of the clan.