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•Analyses showed resolution among 1/3 of the Diospyros species form NC clade III.•Some morphological distinct species could not be discriminated with the markers used.•Diospyros ...arrived relative recently (5–20mya) in New Caledonia.•Chromosome counts confirmed the investigated species to be diploid.•Genome sizes varied nearly fourfold among species examined.
To clarify phylogenetic relationships among New Caledonian species of Diospyros, sequences of four plastid markers (atpB, rbcL, trnK–matK and trnS–trnG) and two low-copy nuclear markers (ncpGS and PHYA) were analysed. New Caledonian Diospyros species fall into three clades, two of which have only a few members (1 or 5 species); the third has 21 closely related species for which relationships among species have been mostly unresolved in a previous study. Although species of the third group (NC clade III) are morphologically distinct and largely occupy different habitats, they exhibit little molecular variability. Diospyros vieillardii is sister to the rest of the NC clade III, followed by D. umbrosa and D. flavocarpa, which are sister to the rest of this clade. Species from coastal habitats of western Grande Terre (D. cherrieri and D. veillonii) and some found on coralline substrates (D. calciphila and D. inexplorata) form two well-supported subgroups. The species of NC clade III have significantly larger genomes than found in diploid species of Diospyros from other parts of the world, but they all appear to be diploids. By applying a molecular clock, we infer that the ancestor of the NC clade III arrived in New Caledonia around 9million years ago. The oldest species are around 7million years old and the youngest ones probably much less than 1million years.
Abstract
Applying molecular (AFLP and sequences of nuclear ribosomal ITS), karyological (relative genome size estimations and chromosome counts) and morphometric methods we explored the origin of ...Italian endemic Euphorbia gasparrinii. AFLP data inferred three phylogeographic groups corresponding to Balkan-Central European-northern Italian E. verrucosa, Italian E. gasparrinii and Iberian E. flavicoma. Genetic differentiation among the three species is weak, suggesting their relatively recent divergence. Karyological analyses revealed that populations of E. gasparrinii have 2n = 16 chromosomes, whereas the other two taxa have 2n = 14. This, with weak genetic differentiation and allopatric distribution, supports its recognition as an independent species, despite its weak morphological differentiation. Our study also revealed multiple autopolyploidization events within all three taxa. Contrary to the diploid Apennine populations, the single currently known Sicilian population of E. gasparrinii is tetraploid. It is critically endangered, as the Sicilian distribution has decreased significantly during the past century. Our study underlines the importance of southern European peninsulas as refugial areas during the Pleistocene and provides additional evidence that Mediterranean high mountain plants are suffering severe range contractions due to climate warming.
Abstract
Subtribe Vrieseinae comprise four genera, Alcantarea, Stigmatodon, Vriesea s.s. and Waltillia, encompassing c. 20% of species in Tillandsioideae (Bromeliaceae), almost all of which are ...exclusive to Brazil. Here, we explore the biogeographic history of Vrieseinae, sampling 21 of the 22 genera of Tillandsioideae (130 terminals) and three DNA sequence markers (two plastid: rps16-trnK and matK; one nuclear: PHYC). We inferred a dated phylogeny and the ancestral areas of this lineage through RASP (reconstruct ancestral state in phylogeny) analyses. Vrieseinae were recovered as monophyletic, but tribe Vrieseeae (subtribe Vrieseinae + subtribe Cipuropsidinae) were not. A vicariant event between the Andes and Brazilian Shield probably occurred c. 10 Mya, when two clades, Cipuropsidineae + Tillandsieae and Vrieseineae, diverged. The Atlantic Forest plus the Chacoan region is recognized as the ancestral area for Vrieseinae. The results confirmed the recent origin of genera of Vrieseinae, with estimated crown ages in the Pliocene (5.3–2.6 Mya). We propose that the Paranaean Sea influenced the divergence of the main clades; Pleistocene events were probably responsible for the diversification of the most recent clades. This study sheds light on the biogeographic history of a key group of Neotropical plants, providing a new hypothesis for the evolution of bromeliads.
•The first phylogeny of the bromeliad genus Orthophytum is here presented.•In the present study was sampled 40 of the about 60 recognized species of Orthophytum.•The two main morphological groups of ...Orthophytum arise as non-monophyletic.•The pedunculate inflorescence in the genus can be regarded as derived condition.
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The saxicolous genus Orthophytum (∼60 species, Bromeliaceae) is endemic to eastern Brazil and diversified in xeric habitats of the Atlantic Rainforest, Caatinga and campos rupestres. Within the genus, two main groups are discerned based on the presence or absence of a pedunculate inflorescence, which are further subdivided into several morphological subgroups. However, these systematic hypotheses have not yet been tested in a molecular phylogenetic framework. Here we present the first phylogenetic analysis of Orthophytum using nuclear and plastid markers (phytochrome C, and trnH-psbA and trnL-trnF spacers). Forty species representing the two main groups and all subgroups of Orthophytum, and the related genera Cryptanthus (8 spp.) and Lapanthus (2 spp.) were analyzed. The phylogenetic reconstruction revealed a well-supported clade termed Eu-Orthophytum, containing species with pedunculate inflorescences only. The Orthophytum species with sessile inflorescence formed two clades: (1) the amoenum group and (2) the vagans group plus O. foliosum, the only pedunculate Orthophytum species found outside Eu-Orthophytum. The vagans clade is in sister group position to Eu-Orthophytum. Within the latter, the subgroup mello-barretoi was sister to the most diversified clade, termed Core Orthophytum. Morphological character state reconstructions of floral characters used in previous taxonomic treatments as key diagnostic characters (penduncle presence, corolla form, and petal appendage form) showed different levels of homoplasy.
We aimed to clarify phylogenetic relationships within the pantropical genus
Diospyros (Ebenaceae
sensu
lato), and ascertain biogeographical patterns in the New Caledonian endemic species. We used DNA ...sequences from eight plastid regions (
rbcL,
atpB,
matK,
ndhF,
trnK intron,
trnL intron,
trnL-
trnF spacer, and
trnS-trnG spacer) and included 149 accessions representing 119
Diospyros species in our analysis. Results from this study confirmed the monophyly of
Diospyros with good support and provided a clearer picture of the relationships within the genus than in previous studies. Evidence from phylogenetic analyses suggests that
Diospyros colonized New Caledonia multiple times. The four lineages of
Diospyros in New Caledonia also differ in their degree of diversification. The molecular data indicate that one lineage is paleoendemic and derived from an ancient Australian species. The other three lineages are more closely related to several Southeast Asian species; two of them are neoendemics, and one has radiated rapidly and recently.
Premise of the study: PCR amplification of the matK barcoding region is often difficult when dealing with multiple angiosperm families. We developed a primer cocktail to amplify this region ...efficiently across angiosperm diversity. Methods and Results: We developed 14 matK primers (seven forward, seven reverse) for multiplex PCR, using sequences available in GenBank for 178 taxa belonging to 123 genera in 41 families and 18 orders. Universality of these new multiplexed primers was tested with 53 specimens from 44 representative angiosperm families in 23 different orders. Our primers showed high PCR amplification and sequencing success. Conclusions: These results show that our newly developed primers are highly effective for multiplex PCR and can be employed in future barcode projects involving taxonomically diverse samples across angiosperms. Using multiplex primers for barcoding will reduce the cost and time needed for PCR amplification.
The goal of this study was to tackle two questions related to the systematics of small-flowering Euphrasia species from the Eastern Alps. Our first aim was to test the hypothesis of a wider ...distribution of diploid E. inopinata, considered endemic to the uppermost Ötztal valley in Austria based on ploidy screening of ca. 70 populations along a latitudinal transect. We failed to find new populations of E. inopinata but during the sampling campaign, a diploid population was detected in the eastern Ortler/Ortles mountain range (Italy), which could neither be assigned to E. inopinata nor to E. minima. Thus, our second aim was to clarify, based on a comprehensive sampling of individuals and the use of Amplified Fragment Length Polymorphisms (AFLPs) and/or morphometric data, if this diploid population is morphologically and genetically consistently divergent from both, tetraploid widespread E. minima and E. inopinata. As this was confirmed, we established the relationships of the new entity based on Internal Transcribed Spacer sequences, which uncovered a close relationship with E. minima and describe it here as a new diploid species, E. ultima, which, based on current knowledge, is locally endemic even if a bigger distribution area appears likely.
The contrasting evolutionary histories of endemic versus related cosmopolitan species provide avenues to understand the spatial drivers and limitations of biodiversity. Here, we investigated the ...evolutionary history of three New Zealand endemic
species, and how they are related to cosmopolitan
. We used RADseq to test species delimitations, infer a dated species tree, and investigate gene flow patterns between the New Zealand endemics and the
populations of New Zealand, Australia and Korea. Whole plastid DNA analysis was performed on a larger worldwide sampling. Morphometrics of selected characters were applied to New Zealand sampling. Our RADseq review of over 55 Mbp showed the endemics as genetically well-defined from each other. Their last common ancestor with
lived during the last ten MY. The New Zealand
appears in a clade with Australian and Korean samples. Whole plastid DNA analysis revealed the endemics as members of a southern hemisphere clade, excluding the extant
of New Zealand. Both data provided strong evidence for hybridization between
and
. Our findings provide evidence for at least two migration events of the genus
to New Zealand and hybridization between
and endemic taxa.
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•A densely sampled phylogeny of Phyteuma (Campanulaceae) is reconstructed.•Phyteuma is monophyletic and contains two main clades.•Distinctness of the currently recognized species is ...mostly corroborated.•Dysploidy, allopatric and ecological differentiation drive species differentiation.
Phyteuma is a chromosomally and ecologically diverse vascular plant genus and constitutes an excellent system for studying both the role of chromosomal change for species diversification and the evolution of high-mountain biota. This kind of research is, however, hampered by the lack of a sound phylogenetic framework exacerbated by the notoriously low predictive power of traditional taxonomy with respect to phylogenetic relationships in Campanulaceae. Based on a comprehensive taxon sampling and analyses of nuclear and plastid sequence and AFLP fingerprint data, Phyteuma is confirmed as a monophyletic group sister to the monotypic Physoplexis, which is in line with their peculiar flower morphologies. Within Phyteuma two clades, largely corresponding to previously recognized sections, are consistently found. The traditional circumscription of taxonomic series is largely rejected. Whereas distinctness of the currently recognized species is mostly corroborated, some interspecific relationships remain ambiguous due to incongruences between nuclear and plastid data. Major forces for diversification and evolution of Phyteuma are descending dysploidy (i.e., a decrease in chromosome base number) as well as allopatric and ecological differentiation within the Alps, the genus’ center of species diversity.
Abstract
In this review article, we provide an overview of the status of research on Old World Ebenaceae with an emphasis on the large genus Diospyros. The well-supported phylogenetic tree obtained ...from nucleotide sequences of multiple regions of plastid genome gave clear insights into the subfamilial classification of Ebenaceae. It supported inclusion of previously recognized genera such as Cargillia, Gunisanthus, Maba, Macreightia and Tetraclis in Diospyros. Endemic Diospyros spp. of New Caledonia have multiple origins. One of these clades has c. 21 species that are morphologically distinct and occupy different ecological niches, but they exhibit low genetic variation, leading to a lack of phylogenetic resolution. Analyses of whole plastid genome sequences did not greatly increase resolution or support for results of our previous plastid analyses. Geographical clustering of the individuals against a background of lower sequence divergence of the whole plastid genome could be due to transfer of plastid genomes during hybridization and introgression following secondary contact. However, > 8400 filtered single nucleotide polymorphisms (SNPs) from restriction site associated DNA sequencing (RADseq) confirmed species circumscriptions for this clade and produced well-supported phylogenetic relationships, pointing to an early regional clustering among populations and species. This supported allopatric speciation with respect to macrohabitat (i.e. climatic conditions) having had a role in the initial differentiation in the group. A later, more rapid radiation involved divergence with respect to microhabitat (e.g. soil preference). Although chromosome counts indicate that Diospyros spp. are consistently diploids with 2n = 30, extensive variation in genome size has been observed, which is due to an increase of repeat elements, including LTR/gypsy. In Ebenaceae, pollen is heterogeneous, and palynological synapomorphies are traced at different taxonomic levels. Several new Diospyros spp. have recently been identified and documented from India, Thailand, China, Africa and New Caledonia. Taxonomic revisions have been completed for the Australian species, and synonyms are reported for some New Caledonian Diospyros spp.
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