Plastidial Markers Research Articles

La anatomía de la raíz como evidencia filogenética para los helechos Cheilanthoides (Pteridaceae)

Background and aims: To our hypothesis on the evolutionary relationships of Cheilanthoid ferns, based on molecular data and partially on morphological and reproductive data, we add here a study of root anatomy in the genera of the subfamily occurring in South America. M&M: Root characters were analyzed anatomically in 48 South American species representing the 12 genera of Cheilanthoideae occurring in South America. Techniques of plant histology were used for anatomical analysis and tissue characterization. Characters with possible diagnostic value were identified and mapped on a molecular phylogeny of Cheilanthoideae based on three plastidial markers (rbcL, trnL-F and rps4). Results: The character "type of root cortex" showed a distribution of states that fit to the major clades or genera in the phylogeny of the subfamily. The homogeneous cortex state was plesiomorphic for Cheilanthoideae, whereas the heterogeneous bark state was acquired by some genera of the hemionitoid clade: Hemionitis and the genera of the Adiantopsis-Doryopteris clade (except Mineirella). In addition, we discuss the role of different tissues in the root mechanics of this group. Conclusions: The character "type of root cortex" could contribute to the characterization of genera and the generic assignment of confusing species in the classification of Cheilanthoideae. However, the complete resolution of the relationship of hemionitds clade in the global phylogeny of the subfamily is necessary.

Hymenophyllum subg. Hymenophyllum (Hymenophyllaceae) in the Atlantic Forest Domain, Brazil: Phylogenetic Relationships and Taxonomic Review

Abstract— A revision of the species of Hymenophyllum subg. Hymenophyllum in the Brazilian Atlantic Forest domain is presented. Morphological and molecular analyses were performed based on herbarium material and samples collected during fieldwork. Molecular analyses were performed with data of the plastidial markers rbcL, rbcL-accD, rps4-trnS, and trnG-R. The results demonstrate the existence of three distinct and independent lineages of H. subgenus Hymenophyllum in the Atlantic Forest domain. Three taxa were recognized: H. fucoides, H. megachilum, and a new species, H. bradeanum, endemic to the Itatiaia Massif, southeast Brazil. Distribution maps, identification keys, descriptions, and illustrations are provided, together with a preliminary update of the conservation status of the species.

Molecular phylogenetic tools reveal the phytogeographic history of the genus Capparis L. and suggest its reclassification

Capparis is the largest genus of the family Capparaceae, represented by 142 species in the tropics and subtropics of the Old World. Despite being one of the medicinally and economically important genera with its unique distribution pattern, the evolutionary history of Capparis remained unexplored. Moreover, the phylogenetic relationships, origin, dispersal, and character evolution of the genus were poorly understood. With the objectives to (i) test the congruence between the molecular and morphological datasets, (ii) validate Jacobs' hypothesis on the origin, dispersal, and speciation pattern of Capparis using new fossil data, and (iii) understand the possible evolutionary role of some key morphological characters, we sampled across the five speciation centres of Capparis. The results derived from three plastidial markers (matK, trnL-F and rbcL) revealed incongruence with the morphology based delimitations and suggested a new sectional classification in Capparis. Divergence dating analysis revealed that Capparaceae originated in Africa at 47.25 MYA and Capparis in Peninsular India at about 29.32 MYA. Capparis followed multiple forward and backward dispersal, supporting the “into and out of India” hypothesis. These dispersal events were consistent with the various land bridges in different parts of the Old World during the Eocene to Miocene. The only long-distance dispersal event was observed in the case of the New World Capparaceae, corroborating the earlier findings. Our results suggest West Asia to the North African region as another centre of speciation for Capparis and present a robust age estimate for the genus. The character state reconstruction of Capparis revealed a unique evolutionary adaptation due to exposure to various climatic conditions and the acquisition of suitable pollination strategies. We hypothesize that the gynophore length, sepal shape, and blotches on petals contribute substantially to the pollination success.

Species Complexes in Capparis (Capparaceae) Resolved with Plastidial Markers

Capparis with about 142 taxa is the largest genus in the angiosperm family Capparaceae, and is of high medicinal and economic importance. Several taxa such as C. cartilaginea, C. cleghornii, C. incanescens, C. moonii, C. roxburghii, C. sepiaria, C. spinosa and C. spinosa subsp. himalayensis are difficult to distinguish from each other based on morphology, and they all have partly overlapping geographic distributions. This study assesses the potential of four plastidial loci (rbcL, matK, trnL-trnF, and psbA-trnH) to resolve three species complexes in Capparis. Successful amplification and sequencing, as well as statistical analyses, revealed matK, trnL-trnF, and their combination to be the most effective DNA markers. With these markers we were able to distinguish different Capparis taxa collected from their natural habitats and from the crude drug market. The species rank of C. himalayensis was reinstated based on morphology and molecular data. The phylogenetic relationships of the poorly known C. danielii and C. incanescens with C. sepiaria were clarified.

EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives.

Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. Methods: In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms. Results: Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported. Conclusion: This deep EST–SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.

<p><strong>Rock star flowers: <em>Conchocarpus hendrixii </em>(Galipeinae, Rutaceae), a new species from Eastern Brazil with notes on its phylogenetic position in the genus</strong></p>

A new species, Conchocarpus hendrixii (tribe Galipeinae, Rutaceae), is described and illustrated. To date, this new species is known from populations observed in the municipalities of Cardoso Moreira and São Fidélis in Serra da Bandeira/Serra da Vista mountain ranges in northern Rio de Janeiro state in the Atlantic Rainforest biome and was brought to light as an undescribed species thanks to photographs shared on the social media site Facebook. The epithet “hendrixii” is in honor of Jimi Hendrix, guitarist and singer-songwriter, who wrote the song “Purple Haze,” in reference to the purple color of the flowers of the new species. Analyzes showed that flowers of the new species bear a staminal tube, a characteristic present only in C. odoratissimus among the Conchocarpus. However, this species bears flowers with much shorter staminal tubes (c. 2–2.5 mm in length v. 1–1.2 cm in the new species) and smaller flowers, among other morphologically dissimilar characteristics. Molecular phylogenetic analysis using nuclear (ITS-1 and IT-2) and plastidial markers (trnL-trnF and rps16 intron) were conducted and demonstrated that the new species belongs to an internal clade in Conchocarpus, together with species formerly assigned to Almeidea (currently included in Conchocarpus). The presence of pantoporate pollen grains, a synapomorphic trait to this clade supports the molecular results. Conservation status as well as data from foliar and floral (with an emphasis on the staminal tube) anatomy are presented.

New insights into adaptation and population structure of cork oak using genotyping by sequencing.

Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species' evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, "Genotyping by sequencing" is used to derive 1,996 single nucleotide polymorphism markers to assess the species' evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species' genetic background, and to forecast how Q.suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species' gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. "Risk of Non-Adaptedness" (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms.

Insights into the evolutionary dynamics of Neotropical biomes from the phylogeography and paleodistribution modeling of Bromelia balansae.

Historical abiotic and biotic factors have strongly affected species diversification and speciation. Although pre-Pleistocene events have been linked to the divergence of several Neotropical organisms, studies have highlighted a more prominent role of Pleistocene climatic oscillations in shaping current patterns of genetic variation of plants. We performed phylogeographic analyses based on plastidial markers and modeled the current distribution and paleodistribution of Bromelia balansae (Bromeliaceae), an herbaceous species with a wide geographical distribution in South America, to infer the processes underlying its evolutionary history. Combined molecular and paleodistributional modeling analyses indicated retraction during the Last Glacial Maximum followed by interglacial expansion. Populations occurring in the semideciduous Atlantic Forest and the Cerrado formed two distinct genetic clusters, which have been historically or ecologically isolated since late Pliocene to early Pleistocene. Populations located in the transition zone had higher levels of genetic diversity, as expected by the long-term climatic stability in the region detected in our ecological niche models. Our study adds important information on how herbaceous species have been affected by past climate in Central and Southeast Brazil, helping to disentangle the complex processes that have triggered the evolution of Neotropical biota.

Identification of poisonous plants by DNA barcoding approach

The plant exposures are one of the most frequent poisonings reported to poison control centres. The diagnosis of intoxicated patients is usually based on the morphological analysis of ingested plant portions; this procedure requires experience in systematic botany, because the plant identification is based on few evident traits. The objective of this research is to test DNA barcoding approach as a new universal tool to identify toxic plants univocally and rapidly. Five DNA barcode regions were evaluated: three cpDNA sequences (trnH-psbA, rpoB and matK) and two nuclear regions (At103 and sqd1). The performance of these markers was evaluated in three plant groups: (1) a large collection of angiosperms containing different toxic substances, (2) congeneric species showing different degrees of toxicity and (3) congeneric edible and poisonous plants. Based on assessments of PCR, sequence quality and resolution power in species discrimination, we recommend the combination of plastidial and nuclear markers to identify toxic plants. Concerning plastidial markers, matK and trnH-psbA showed consistent genetic variability. However, in agreement with CBOL Plant Working Group, we selected matK as the best marker, because trnH-psbA showed some problems in sequences sizes and alignments. As a final and relevant observation, we also propose the combination of matK with a nuclear marker such as At103 to distinguish toxic hybrids form parental species. In conclusion, our data support the claim that DNA barcoding is a powerful tool for poisonous plant identifications.