Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms

Climatic niche evolution and niche conservatism of Nymphaea species in Africa, South America, and Australia

BACKGROUND

Interest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea's niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models.

RESULTS

There was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures).

CONCLUSION

Our study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.

On the importance of sequence alignment inspections in plastid phylogenomics - an example from revisiting the relationships of the water-lilies

The water-lily clade represents the second earliest-diverging branch of angiosperms. Most of its species belong to Nymphaeaceae, of which the "core Nymphaeaceae"-comprising the genera Euryale, Nymphaea and Victoria-is the most diverse clade. Despite previous molecular phylogenetic studies on the core Nymphaeaceae, various aspects of their evolutionary relationships have remained unresolved. The length-variable introns and intergenic spacers are known to contain most of the sequence variability within the water-lily plastomes. Despite the challenges with multiple sequence alignment, any new molecular phylogenetic investigation on the core Nymphaeaceae should focus on these noncoding plastome regions. For example, a new plastid phylogenomic study on the core Nymphaeaceae should generate DNA sequence alignments of all plastid introns and intergenic spacers based on the principle of conserved sequence motifs. In this investigation, we revisit the phylogenetic history of the core Nymphaeaceae by employing such an approach. Specifically, we use a plastid phylogenomic analysis strategy in which all coding and noncoding partitions are separated and then undergo software-driven DNA sequence alignment, followed by a motif-based alignment inspection and adjustment. This approach allows us to increase the reliability of the character base compared to the default practice of aligning complete plastomes through software algorithms alone. Our approach produces significantly different phylogenetic tree reconstructions for several of the plastome regions under study. The results of these reconstructions underscore that Nymphaea is paraphyletic in its current circumscription, that each of the five subgenera of Nymphaea is monophyletic, and that the subgenus Nymphaea is sister to all other subgenera of Nymphaea. Our results also clarify many evolutionary relationships within the Nymphaea subgenera Brachyceras, Hydrocallis and Nymphaea. In closing, we discuss whether the phylogenetic reconstructions obtained through our motif-based alignment adjustments are in line with morphological evidence on water-lily evolution.

Generic concepts and species diversity within the Gynoxyoid clade (Senecioneae, Compositae)

The Gynoxyoid clade of the Senecioneae (Asteraceae) until now included the five genera Aequatorium, Gynoxys, Nordenstamia, Paracalia and Paragynoxys as diagnosed using selected morphological characters. In their pre-phylogenetic circumscription, the genera Aequatorium and Paragynoxys were considered to inhabit the northern Andes in contrast to Nordenstamia and Paracalia that occur in the central Andes. The most species-rich genus, Gynoxys, was believed to be distributed throughout the Andes. We use a recently established plastid phylogenomic framework that rendered Gynoxys paraphyletic to further evaluate the delimitation of genera in the Gynoxyoid clade. We examine the morphological variation of all members of the Gynoxyoid to identify characters potentially informative at genus level. This results in a matrix of eleven, mostly multistate characters, including those originally used to diagnose these genera. The ancestral character state inference displays a high level of homoplasy, but nevertheless supports the recognition of four genera. Aequatorium is characterised by white radiate capitula. Paracalia and Paragynoxys share white flowers and floral characteristics, such as flower opening and length of disc flowers lobes, as plesiomorphic states, but differ in habit (scandent shrubs vs. trees). Paracalia also retained white flowers, but its two species are characterised by the absence of outer phyllaries. The genera Gynoxys and Nordenstamia comprise species with yellow capitula which appear to be a derived feature in the Gynoxyoids. The genus Nordenstamia, with eight species, is synonymised under Gynoxys since molecular evidence shows its species nested within various parts of the Gynoxys subclade and the morphological variation of Nordenstamia falls well within that of Gynoxys. With the goal to assign all species to four genera (Aequatorium, Gynoxys, Paracalia and Paragynoxys), we assess the states for the eleven characters for all members of the Gynoxyoids and generate new ETS and ITS sequences for 171 specimens belonging to 49 species to further support their generic placement. We provide a taxonomic treatment for the four genera recognised here including amended diagnoses and morphological descriptions. Furthermore, a species-level taxonomic backbone is elaborated for all genera using electronic tools that list 158 currently accepted names and synonyms (209 names in total) with the respective protologue and type information, as well as notes on the current understanding of species limits. Eleven names are newly synonymised, two are lectotypified and eight are newly transferred to other genera.

The diversification of Caribbean Buxus in time and space: elevated speciation rates in lineages that accumulate nickel and spreading to other islands from Cuba in non-obligate ultramafic species

BACKGROUND AND AIMS

The genus Buxus has high levels of endemism in the Caribbean flora, with ~50 taxa. In Cuba, 82 % grow on ultramafic substrates and 59 % are nickel (Ni) accumulators or Ni hyperaccumulators. Hence it is an ideal model group to study if this diversification could be related to adaptation to ultramafic substrates and to Ni hyperaccumulation.

METHODS

We generated a well-resolved molecular phylogeny, including nearly all of the Neotropical and Caribbean Buxus taxa. To obtain robust divergence times we tested for the effects of different calibration scenarios, and we reconstructed ancestral areas and ancestral character states. Phylogenetic trees were examined for trait-independent shifts in diversification rates and we used multi-state models to test for state-dependent speciation and extinction rates. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America'.

KEY RESULTS

We found a Caribbean Buxus clade with Mexican ancestors, encompassing three major subclades, which started to radiate during the middle Miocene (13.25 Mya). Other Caribbean islands and northern South America were reached from ~3 Mya onwards.

CONCLUSIONS

An evolutionary scenario is evident in which Buxus plants able to grow on ultramafic substrates by exaptation became ultramafic substrate endemics and evolved stepwise from Ni tolerance through Ni accumulation to Ni hyperaccumulation, which has triggered species diversification of Buxus in Cuba. Storms could have contributed to Cuba acting as a species pump and to Buxus reaching other Caribbean islands and northern South America'.

Structural Diversities and Phylogenetic Signals in Plastomes of the Early-Divergent Angiosperms: A Case Study in Saxifragales

As representative of the early-divergent groups of angiosperms, Saxifragales is extremely divergent in morphology, comprising 15 families. Within this order, our previous case studies observed significant structural diversities among the plastomes of several lineages, suggesting a possible role in elucidating their deep phylogenetic relationships. Here, we collected 208 available plastomes from 11 constituent families to explore the evolutionary patterns among Saxifragales. With thorough comparisons, the losses of two genes and three introns were found in several groups. Notably, 432 indel events have been observed from the introns of all 17 plastomic intron-containing genes, which could well play an important role in family barcoding. Moreover, numerous heterogeneities and strong intrafamilial phylogenetic implications were revealed in pttRNA (plastomic tRNA) structures, and the unique structural patterns were also determined for five families. Most importantly, based on the well-supported phylogenetic trees, evident phylogenetic signals were detected in combinations with the identified pttRNAs features and intron indels, demonstrating abundant lineage-specific characteristics for Saxifragales. Collectively, the results reported here could not only provide a deeper understanding into the evolutionary patterns of Saxifragales, but also provide a case study for exploring the plastome evolution at a high taxonomic level of angiosperms.

Molecular Identification of African Nymphaea Species (Water Lily) Based on ITS, trnT-trnF and rpl16

The genus Nymphaea L. (water lily) is the most diverse genus in the family Nymphaeaceae, with more than 50 species worldwide, including 11 species distributed in Africa. The complex and variable morphology of Nymphaea makes it extremely difficult to accurately identify species based on morphological characteristics alone. DNA barcoding has the potential to identify species accurately. In this study, 158 Nymphaea populations from seven African countries were collected for species identification by ITS, trnT-trnF and rpl16. Additionally, the three candidate DNA barcodes were evaluated for genetic distance and barcoding gap. Based on the comprehensive analysis of sequence similarity, genetic distance method and phylogenetic tree, a total of 137 populations of seven Nymphaea species from African were well-identified, including N. lotus, N. petersiana, N. zenkeri, N. nouchali var. caerulea, N. micrantha and N. guineensis. ITS has more obvious advantages over trnT-trnF, rpl16 and trnT-trnF+rpl16 in the intraspecific and interspecific variation differences and barcoding gap and can identify most species. trnT-trnF and rpl16 can identify some species that cannot be identified by ITS. The results showed that it is more appropriate to apply the combination of ITS and trnT-trnF (or rpl16) as the DNA barcoding of Nymphaea. Additionally, this study further enriches the DNA barcoding database of Nymphaea and provides a reference basis for studying taxonomy, phylogenetics and evolutionary origin of Nymphaea.

Middle Miocene lotus (Nelumbonaceae, Nelumbo) from the Qaidam Basin, Northern Tibet Plateau

The Neogene environment and paleovegetation of today’s semi-arid and arid Central Asia remain elusive. Little is known about the effect of paleoclimatic change on the distribution and ecological response mechanisms of aquatic plants, especially on the Tibetan Plateau. Here, we report a new species of Nelumbo Adanson, including leaves, receptacles, and fruits, namely Nelumbo delinghaensis sp. nov., from the Upper Youshashan Formation of the upper Middle Miocene in the northern Qaidam Basin on the Tibetan Plateau. The new species comprises centrally peltate leaves with 12−15 actinodromous primary veins and a receptacle embedded with ca. 15−30 fruits, with an unlobed central disc. Megafossils of lotus from northwest China broaden the geographical and stratigraphic ranges of Nelumbo. Our findings suggest that a large freshwater lake body surrounded by temperate forests and grassland developed in the Qaidam Basin during the late Middle Miocene, in sharp contrast to the present desert vegetation. The climate used to be sufficiently warm and moist enough to support a forest-steppe ecosystem with abundant freshwater bodies.

Development of a multiprimer metabarcoding approach to understanding trophic interactions in agroecosystems

To understand trophic interactions and the precise ecological role of each predatory species, it is important to know which arthropod and plant resources are used by generalist predators in agroecosystems. Molecular approaches, such as the use of high-throughput sequencing (HTS), play a key role in identifying these resources. This study develops a multiprimer metabarcoding approach for screening the most common trophic interactions of two predatory arthropods with contrasting morphologies, Rhagonycha fulva (Coleoptera: Cantharidae) and Anthocoris nemoralis (Hemiptera: Anthocoridae) collected from a peach crop. To reduce the time and cost of this metabarcoding approach, we first evaluated the effect of using two different predator-pools of different size (10 and 23 individuals of the same species). We also used our system to analyze the performance of one and two primer pairs in the same library. Our results show that the analysis of 23 individuals together with the use of two primer pairs in the same library optimize the HTS analysis. Using these best-performing conditions, we then analyzed the entire bodies of field-collected predators as well as the washing solutions used to clean the insect bodies. We were able to identify both gut content (i.e., diet) and external pollen load (i.e., on the insects' bodies). This study also demonstrates the importance of washing predatory insects' bodies prior to HTS analysis when the target species have a considerable size (>10 mm) and hairy structures. This metabarcoding approach has significant potential for the study of trophic links in agriculture, revealing expected and unexpected trophic relationships.

Software Choice and Sequencing Coverage Can Impact Plastid Genome Assembly-A Case Study in the Narrow Endemic Calligonum bakuense

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequencing coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequencing coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense compared to congeners. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and seven levels of sequencing coverage across the plastid genome (original sequencing depth, 2,000x, 1,000x, 500x, 250x, 100x, and 50x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic reconstruction is assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produces the most consistent assemblies for C. bakuense. Moreover, we demonstrate that a sequencing coverage between 500x and 100x can reduce both the sequence variability across assembly contigs and computation time. When comparing the most reliable plastid genome assemblies of C. bakuense, a sequence difference in only three nucleotide positions is detected, which is less than the difference potentially introduced through software choice.

Taxonomy of Dianthus (Caryophyllaceae) - overall phylogenetic relationships and assessment of species diversity based on a first comprehensive checklist of the genus

In this study, we present an overall phylogenetic framework for Dianthus using four plastid regions (matK-trnK-psbA, rpl32-trnL, trnQ-rps16) and nuclear ITS and a species-level checklist for the genus developed by using all available databases and the literature. The trees from the plastid dataset depict a clade of Dianthus that also includes Velezia and a few taxa of Petrorhagia. New combinations in Dianthus are provided for these species. The checklist of Dianthus in this new delimitation covers 1781 names, with 384 accepted species, 150 subspecies, 12 heterotypic varieties and two forms (not counting autonyms), 1050 synonyms, 22 hybrid names and 172 unresolved names, 3 names were excluded. Implications for the evolution of flower characters, life forms, biogeography, as well as sectional classification are discussed based on the phylogenetic framework.

The evolution of the Aristolochia pallida complex (Aristolochiaceae) challenges traditional taxonomy and reflects large‐scale glacial refugia in the Mediterranean

The taxonomy of the Mediterranean Aristolochia pallida complex has been under debate since several decades with the following species currently recognized: A. pallida, A. lutea, A. nardiana, A. microstoma, A. merxmuelleri, A. croatica, and A. castellana. These taxa are distributed from Iberia to Turkey. To reconstruct phylogenetic and biogeographic patterns, we employed cpDNA sequence variation using both noncoding (intron and spacer) and protein‐coding regions (i.e., trnK intron, matK gene, and trnK‐psbA spacer). Our results show that the morphology‐based traditional taxonomy was not corroborated by our phylogenetic analyses. Aristolochia pallida, A. lutea, A. nardiana, and A. microstoma were not monophyletic. Instead, strong geographic signals were detected. Two major clades, one exclusively occurring in Greece and a second one of pan‐Mediterranean distribution, were found. Several subclades distributed in Greece, NW Turkey, Italy, as well as amphi‐Adriatic subclades, and a subgroup of southern France and Spain, were revealed. The distribution areas of these groups are in close vicinity to hypothesized glacial refugia areas in the Mediterranean. According to molecular clock analyses the diversification of this complex started around 3–3.3 my, before the onset of glaciation cycles, and the further evolution of and within major lineages falls into the Pleistocene. Based on these data, we conclude that the Aristolochia pallida alliance survived in different Mediterranean refugia rarely with low, but often with a high potential for range extension, and a high degree of morphological diversity.

The Genetic Diversity of Enset (Ensete ventricosum) Landraces Used in Traditional Medicine Is Similar to the Diversity Found in Non-medicinal Landraces

Enset (Ensete ventricosum) is a multipurpose crop extensively cultivated in southern and southwestern Ethiopia for human food, animal feed, and fiber. It has immense contributions to the food security and rural livelihoods of 20 million people. Several distinct enset landraces are cultivated for their uses in traditional medicine. These landraces are vulnerable to various human-related activities and environmental constraints. The genetic diversity among the landraces is not verified to plan conservation strategy. Moreover, it is currently unknown whether medicinal landraces are genetically differentiated from other landraces. Here, we characterize the genetic diversity of medicinal enset landraces to support effective conservation and utilization of their diversity. We evaluated the genetic diversity of 51 enset landraces, of which 38 have reported medicinal value. A total of 38 alleles across the 15 simple sequence repeat (SSR) loci and a moderate level of genetic diversity (He = 0.47) were detected. Analysis of molecular variation (AMOVA) revealed that only 2.4% of the total genetic variation was contributed by variation among the medicinal and non-medicinal groups of landraces, with an FST of 0.024. A neighbor-joining tree showed four separate clusters with no correlation to the use-values of the landraces. Except for two, all "medicinal" landraces with distinct vernacular names were found to be genetically different, showing that vernacular names are a good indicator of genetic distinctiveness in these specific groups of landraces. The discriminant analysis of the principal components also confirmed the absence of distinct clustering between the two groups. We found that enset landraces were clustered irrespective of their use-value, showing no evidence for genetic differentiation between the enset grown for 'medicinal' uses and non-medicinal landraces. This suggests that enset medicinal properties may be restricted to a more limited number of genotypes, might have resulted from the interaction of genotype with the environment or management practice, or partly misreported. The study provides baseline information that promotes further investigations in exploiting the medicinal value of these specific landraces.

Plastid phylogenomics of the Gynoxoid group (Senecioneae, Asteraceae) highlights the importance of motif-based sequence alignment amid low genetic distances

PREMISE

The genus Gynoxys and relatives form a species-rich lineage of Andean shrubs and trees with low genetic distances within the sunflower subtribe Tussilaginineae. Previous molecular phylogenetic investigations of the Tussilaginineae have included few, if any, representatives of this Gynoxoid group or reconstructed ambiguous patterns of relationships for it.

METHODS

We sequenced complete plastid genomes of 21 species of the Gynoxoid group and related Tussilaginineae and conducted detailed comparisons of the phylogenetic relationships supported by the gene, intron, and intergenic spacer partitions of these genomes. We also evaluated the impact of manual, motif-based adjustments of automatic DNA sequence alignments on phylogenetic tree inference.

RESULTS

Our results indicate that the inclusion of all plastid genome partitions is needed to infer well-supported phylogenetic trees of the Gynoxoid group. Whole plastome-based tree inference suggests that the genera Gynoxys and Nordenstamia are polyphyletic and form the core clade of the Gynoxoid group. This clade is sister to a clade of Aequatorium and Paragynoxys and also includes some but not all representatives of Paracalia.

CONCLUSIONS

The concatenation and combined analysis of all plastid genome partitions and the construction of manually-curated, motif-based DNA sequence alignments are found to be instrumental in the recovery of well-supported relationships of the Gynoxoid group. We demonstrate that the correct assessment of homology in genome-level plastid sequence data sets is crucial for subsequent phylogeny reconstruction and that the manual post-processing of multiple sequence alignments improves the reliability of such reconstructions amid low genetic distances between taxa.

DNA Barcoding of Andaliman (Zanthoxylum acanthopodium DC) from North Sumatra Province of Indonesia Using Maturase K Gene

Andaliman (Zanthoxylum acanthopodium DC) is a native plant of North Sumatra province. Zanthoxylum acanthopodium is a member of Rutaceae family widely found in northern Sumatra, Indonesia. The aim of this study was to barcode Z. acanthopodium in North Sumatra province, Indonesia based on cpDNA maturase K (matK). Samples were collected in seven localities across six regions of North Sumatra province. Phylogenetic analysis was conducted using Maximum Likelihood method. The results of phylogenetic analysis indicate that Z. acanthopodium is a monophyletic group that is derived from a common ancestor. The results of the phylogenetic tree construction show that there is a grouping of accession between Z. acanthopodium species separate from other species in the Zanthoxylum genus as well as those of the Rutaceae family. The results showed that cpDNA matK marker can effectively be used as DNA barcoding to identify Z. acanthopodium.

Molecular Genetic Diversity and Population Structure in Ethiopian Chickpea Germplasm Accessions

Chickpea (Cicer arietinum L.) is a cheap source of protein and rich in minerals for people living in developing countries. In order to assess the existing molecular genetic diversity and determine population structures in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on the chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers, and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average number of alleles per locus, polymorphism information content, and expected heterozygosity were 12, 0.684, and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from diverse sources into three evolutionary and/or biological groups (improved desi, improved kabuli, and landraces). The population structure analysis revealed six sub-populations from 118 chickpea genotypes studied. AMOVA revealed that 57%, 29%, and 14% of the total genetic variations were observed among individuals, within populations, and among populations. The insights into the genetic diversity at molecular levels in the Ethiopian germplasm lines can be used for designing conservation strategies as well as the diverse germplasm lines identified in this study can be used for trait dissection and trait improvement.

DNA barcoding of some medicinally important plant species of Lamiaceae family in India

Several species of the Lamiaceae family are the primary source of bioactive aromatic oils and secondary metabolites, having broader applications in the cosmetics, pharmaceuticals, food, confectionery and liquor industries. Due to the scarcity of raw materials and high costs of this family's economically vital species, its products often adulterated to cater to the market's high demand. The present study provides a DNA based approach for identifying different species of this family. Henceforth, the performance of three already proposed barcode loci (matK, trnH-psbA and trnL) was examined for their PCR amplification and species recognition efficacy on various Lamiaceae species and cultivars using three different approaches such as pairwise genetic distance method, BLASTn and phylogenetic tree based on maximum likelihood (ML) analysis. Results illustrate that among all the DNA barcoding loci, matK locus can accurately and efficiently distinguish all the studied species followed by trnH-psbA and trnL. Present investigation may help diminish the illegal trade and events of adulteration of medicinally important plants species in genus Mentha, Ocimum and Plectranthus. This investigation will also help fulfil the scarcity of sequences of barcode loci of these species in the NCBI database. Apart from providing a molecular level reference for identifying processed herbal products, this technique also offers a convenient method for species identification and germplasm conservation of the Lamiaceae family.

Environment, phylogeny, and photosynthetic pathway as determinants of leaf traits in savanna and forest graminoid species in central Brazil

Leaf traits are closely linked to plant responses to the environment and can provide important information on adaptation and evolution. These traits may also result from common ancestry, so phylogenetic relationships also play an important role in adaptive evolution. We evaluated the effects of the closed forest environment (gallery forest) and the open savanna environment (cerrado) on the selection of leaf traits of graminoid species. The two plant communities differ in light, nutrients, and water availability, which are important drivers in the selection and differentiation of these traits. We also investigated the functional structure and the role of phylogeny in the functional organization of species, considering leaf traits. Patterns of leaf trait variation differed between forest and savanna species suggesting habitat specialization. Wider and longer leaves, with higher values of specific leaf area, chlorophyll, and nitrogen, seem to be an advantage for graminoid species growing in forest environments, while thicker leaves, with higher values of leaf dry-matter content and carbon, benefit species growing in savanna environments. We found few phylogenetic signals related to leaf traits in each environment. Therefore, the functional similarity that the gallery forest and cerrado graminoid species share within their group is independent of their phylogenetic proximity. Environmental filters affect the functional structure of communities differently, generating communities with trait values that are more distant than expected by chance in cerrado (functional dispersion), and closer than expected by chance in the gallery forest (functional convergence).

Quaternary diversification of a columnar cactus in the driest place on earth

PREMISE

The cactus family (Cactaceae) is a speciose lineage with an almost entirely New World distribution. The genus Eulychnia with eight currently recognized species is endemic to the Atacama and Peruvian Deserts. Here we investigated the phylogeny of this group based on a complete taxon sampling to elucidate species delimitation and biogeographic history of the genus.

METHODS

A family-wide Bayesian molecular clock dating based on plastid sequence data was conducted to estimate the age of Eulychnia and its divergence from its sister genus Austrocactus. A second data set obtained from genotyping by sequencing (GBS) was analyzed, using the family-wide age estimate as a secondary calibration to date the GBS phylogeny using a penalized likelihood approach. Ancestral ranges were inferred employing the dispersal extinction cladogenesis approach.

RESULTS

Our GBS phylogeny of Eulychnia was fully resolved with high support values nearly throughout the phylogeny. The split from Austrocactus occurred in the late Miocene, and Eulychnia diversified during the early Quaternary. Three lineages were retrieved: Eulychnia ritteri from Peru is sister to all Chilean species, which in turn fall into two sister clades of three and four species, respectively. Diversification in the Chilean clades started in the early Pleistocene. Eulychnia likely originated at the coastal range of its distribution and colonized inland locations several times.

CONCLUSIONS

Diversification of Eulychnia during the Pleistocene coincides with long periods of hyperaridity alternated with pluvial phases. Hyperaridity caused habitat fragmentation, ultimately leading to speciation and resulting in the current allopatric distribution of taxa.

Plastid Genomes of Flowering Plants: Essential Principles

The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.

Genetic Diversity of Orobanche crenata Populations in Ethiopia Using Microsatellite Markers

Orobanche crenata is a parasitic weed that causes considerable yield losses on food legumes in Ethiopia and the Mediterranean region. Understanding the genetic diversity of Orobanche crenata using molecular techniques generate useful information in managing the weed through resistance breeding. This study aimed at assessing the genetic diversity of O. crenata populations collected from major faba bean growing areas of Ethiopia. A total of 96 samples were collected from the Orobanche-infested faba bean farmer field. The genetic diversity of the population was studied using 30 O. cumana SSR markers. The results showed that 11 SSRs were functional and transferable markers to study the diversity of O. crenata populations. The average number of alleles, gene diversity, heterozygosity, and polymorphic information content values for the SSR loci were 9.6, 0.82, 0.38, and 0.80, respectively. The pairwise genetic similarity analysis showed the lowest genetic distance between samples collected from South Gondar and South Wollo (0.12) while the highest genetic distance (0.48) was found between South Gondar and North Wollo. The analysis of molecular variance result indicated that the variation among individuals was a major source of genetic variation (55%) followed by within individuals (43%) and among populations (2%) variation. The output of population genetic structure analysis indicated the presence of two major groups irrespective of the area of collection or region of origin. Besides, the outcome of the spatial autocorrelation computation indicated a significant and positive genetic correlation between samples collected under a 28 km radius. In general, the absence of geographic region based genetic structure presumably demonstrates the expansion of the parasitic weed between farming sites upon its recent introduction to the country. Thus, the clear absence of population differentiation warrants screening faba bean population in hot spot area.

Identification of High Molecular Variation Loci in Complete Chloroplast Genomes of Mammillaria (Cactaceae, Caryophyllales)

In plants, partial DNA sequences of chloroplasts have been widely used in evolutionary studies. However, the Cactaceae family (1500-1800 species) lacks molecular markers that allow a phylogenetic resolution between species and genera. In order to identify sequences with high variation levels, we compared previously reported complete chloroplast genomes of seven species of Mammillaria. We identified repeated sequences (RSs) and two types of DNA variation: short sequence repeats (SSRs) and divergent homologous loci. The species with the highest number of RSs was M. solisioides (256), whereas M. pectinifera contained the highest amount of SSRs (84). In contrast, M. zephyranthoides contained the lowest number (35) of both RSs and SSRs. In addition, five of the SSRs were found in the seven species, but only three of them showed variation. A total of 180 homologous loci were identified among the seven species. Out of these, 20 loci showed a molecular variation of 5% to 31%, and 12 had a length within the range of 150 to 1000 bp. We conclude that the high levels of variation at the reported loci represent valuable knowledge that may help to resolve phylogenetic relationships and that may potentially be convenient as molecular markers for population genetics and phylogeographic studies.

ECuADOR-Easy Curation of Angiosperm Duplicated Organellar Regions, a tool for cleaning and curating plastomes assembled from next generation sequencing pipelines

Background

With the rapid increase in availability of genomic resources offered by Next-Generation Sequencing (NGS) and the availability of free online genomic databases, efficient and standardized metadata curation approaches have become increasingly critical for the post-processing stages of biological data. Especially in organelle-based studies using circular chloroplast genome datasets, the assembly of the main structural regions in random order and orientation represents a major limitation in our ability to easily generate “ready-to-align” datasets for phylogenetic reconstruction, at both small and large taxonomic scales. In addition, current practices discard the most variable regions of the genomes to facilitate the alignment of the remaining coding regions. Nevertheless, no software is currently available to perform curation to such a degree, through simple detection, organization and positioning of the main plastome regions, making it a time-consuming and error-prone process. Here we introduce a fast and user friendly software ECuADOR, a Perl script specifically designed to automate the detection and reorganization of newly assembled plastomes obtained from any source available (NGS, sanger sequencing or assembler output).

Methods

ECuADOR uses a sliding-window approach to detect long repeated sequences in draft sequences, which then identifies the inverted repeat regions (IRs), even in case of artifactual breaks or sequencing errors and automates the rearrangement of the sequence to the widely used LSC–Irb–SSC–IRa order. This facilitates rapid post-editing steps such as creation of genome alignments, detection of variable regions, SNP detection and phylogenomic analyses.

Results

ECuADOR was successfully tested on plant families throughout the angiosperm phylogeny by curating 161 chloroplast datasets. ECuADOR first identified and reordered the central regions (LSC–Irb–SSC–IRa) for each dataset and then produced a new annotation for the chloroplast sequences. The process took less than 20 min with a maximum memory requirement of 150 MB and an accuracy of over 99%.

Conclusions

ECuADOR is the sole de novo one-step recognition and re-ordination tool that provides facilitation in the post-processing analysis of the extra nuclear genomes from NGS data. The program is available at https://github.com/BiodivGenomic/ECuADOR/.

The complete chloroplast genome of Magnolia polytepala: Comparative analyses offer implication for genetics and phylogeny of Yulania

Magnoliaceae is a primitive taxon in the angiosperms, comprising approximately 240 species in 2-17 genera. Many of them have been widely cultivated due to their horticultural and medicinal value. However, there are uncertainties and controversies about the delimitation of the genera except Liriodendron L. in this family. The Yulania taxa is also the focus of dispute at the genus and section levels. In this study, we compared ten Yulania plastomes, including the newly sequenced M. polytepala. The plastome-wide comparative analysis demonstrated that 1) Yulania cp genomes were highly conserved, and the majority differences existed in IR regions with the loss/retention of trnV-GAC or ycf15 gene, 2) mutational hotspots with high levels of nucleotide diversity (Pi > 0.02) existed in both coding (rpoA, and ycf1) and no-coding (ccsA-ndhD, ndhE-ndhG, ndhF-rpl32, petA-psbJ, rpl32-trnL, rps3-rps19, and trnH-psbA) regions among the genus Yulania. Combined with other data from Magnoliaceae plastomes, our reconstructed molecular phylogenetic tree revealed that Yulania is monophyletic, separated from the genus Magnolia L. (=Magnolia subg. Magnolia L.), but seems a sister of Michelia L. Moreover, M. polytepala which belongs to the genus Yulania is most closely related to M. liliiflora. All these results indicated that plastome data may contribute to investigating taxonomy, population genetics and phylogeny of Yulania.

Genetic diversity analysis in Plectranthus edulis (Vatke) Agnew populations collected from diverse geographic regions in Ethiopia using inter-simple sequence repeats (ISSRs) DNA marker system

Background

Plectranthus edulis (Vatke) Agnew (Lamiaceae), locally known as Ethiopian potato syno. Ethiopian dinich, is one of the native Ethiopian edible tuber crops that has been significantly contributing to household food security for millions of subsistence farmers. However, its current production is declining to the extent of total extinction from several administrative regions where it used to be widely cultivated. It is one of the less researched crops regardless of being indigenous and its contribution to food security during time of scarcity. Therefore, we intended to assess the level of genetic diversity in 67 accessions, representing nine populations that were collected from diverse agro-ecologies in the country, using ISSR markers and hence, to generate a baseline information that assists marker assisted breeding, conservation and germplasm management efforts.

Results

In the present study, ten polymorphic ISSR markers were screened and optimized, that generated an average of 7.4 scorable bands per marker and revealed high overall percent polymorphism (95%), Nei’s gene diversity (h = 0.40) and Shannon index (I = 0.62) suggesting ISSR’s effectiveness in detecting high levels of genetic diversity. A considerably high overall populations gene diversity (Nei’s) (h = 0.32) and Shannon index (I = 0.47) were observed, revealing high potential of the populations for further breeding and conservation efforts particularly for population from Gurage administrative zone, which showed the highest values. Similarly, estimation of pairwise genetic distance revealed the importance of cross breeding population from Awi administrative zone to the rest populations. Analysis of hierarchical molecular variance (AMOVA) showed higher levels of genetic differentiation within populations (92%), and collection regions (94%) suggesting that either clonal mode of propagation in the crop or farmers selection pressure for important agronomic traits or both maintained the original heterozygosity in the crop. UPGMA phylogenetic analysis did not strictly group the populations based on their geographic region of origin, which could be attributed to the widely practiced tuber exchange and hence continuous human mediated exchange of genetic material and sharing of the same genetic base among the geographic regions.

Conclusions

The ISSR markers used in the present study were effective in revealing extent and patterns of genetic diversity in P. edulis populations. However, it is important to couple them with agro-morphological traits or codominant molecular markers to get more reliable information for use in breeding and conservation. Several of the potential administrative zones we covered are useful for P. edulis diversification and conservation. However, the crop is currently highly marginalized and this led to rapid decline in population size and loss of valuable agronomic traits. To address this challenge, there is an urgent need to take counteractive measures.

Molecular identification of medicinal plants with amplicon length polymorphism using universal DNA barcodes of the atpF-atpH, trnL and trnH-psbA regions

Amplification success and species discrimination efficiency of universal DNA barcode primers (trnH-psbA, trnL, ycf1b, atpF-atpH, matK and rbcL) was evaluated in 46 representative medicinal plant species of 28 families on agarose gel. The results showed that amplicons length polymorphism revealed by the primers atpF-atpH, trnH-psbA and trnL can simultaneously discriminate all the 46 species under study precisely. Some of the plant species included in this study are used as potential adulterants to other plant species. We were able to successfully discriminate the plant species from their potential substitute. Vitex negundo is an adulterant of Ocimum sanctum which has been successfully discriminated by all these three markers. Another example of adulteration between Bacopa monnieri and Centella asiatica was successfully discriminated by atpF-atpH, trnL and trnH-psbA on the basis of variability in amplicon length of these two medicinal herbs. Further, Cassia tora and Cassia fistula are also adulterants for each other and variability in amplicon length between these two species was revealed by atpF-atpH and trnH-psbA markers. A colour code distance matrix based on amplicon length polymorphism was designed to select primers which can effectively discriminate plants species on the basis of their amplicon length. Discrimination of plant species with the universal markers on agarose gel is a noble and inexpensive approach as it does not require sequencing of amplicons. This procedure will provide a way for the development of diagnostic markers to identify adulteration not only in herbal drug formulations but also in food material.

Zaika, Erst AS, Shepherd KA. Molecular phylogenetic data and seed coat anatomy resolve the generic position of some critical Chenopodioideae (Chenopodiaceae - Amaranthaceae) with reduced perianth segments

The former Chenopodiumsubgen.Blitum and the genus Monolepis (Chenopodioideae) are characterised in part by a reduced (0-4) number of perianth segments. According to recent molecular phylogenetic studies, these groups belong to the reinstated genera Blitum incl. Monolepis (tribe Anserineae) and Oxybasis (tribe Chenopodieae). However, key taxa such as C.antarcticum, C.exsuccum, C.litwinowii, C.foliosumsubsp.montanum and Monolepisspathulata were not included and so their phylogenetic position within the Chenopodioideae remained equivocal. These species and additional samples of Blitumasiaticum and B.nuttallianum were incorporated into an expanded phylogenetic study based on nrDNA (ITS region) and cpDNA (trnL-trnF and atpB-rbcL intergenic spacers and rbcL gene). Our analyses confirm the placement of C.exsuccum, C.litwinowii and C.foliosumsubsp.montanum within Blitum (currently recognised as Blitumpetiolare, B.litwinowii and B.virgatumsubsp.montanum, respectively); additionally, C.antarcticum, currently known as Oxybasisantarctica, is also placed within Blitum (reinstated here as B.antarcticum). Congruent with previous studies, two of the three accepted species of Monolepis - the type species M.trifida (= M.nuttalliana) as well as M.asiatica - are included in Blitum. The monotypic genus Carocarpidium described recently with the type C.californicum is not accepted as it is placed within Blitum (reinstated here as B.californicum). To date, few reliable morphological characters have been proposed that consistently distinguish Blitum (incl. two Monolepis species) from morphologically similar Oxybasis; however, two key differences are evident: (1) the presence of long-petiolate rosulate leaves in Blitum vs. their absence in Oxybasis and (2) a seed coat structure with the outer wall of the testa cells lacking stalactites ('non-stalactite seed coat') but with an obvious protoplast in Blitum vs. seed coat with the outer walls of the testa cells having stalactites ('stalactite seed coat') and a reduced protoplast in Oxybasis. Surprisingly, the newly sequenced North American Monolepisspathulata nested within the tribe Dysphanieae (based on ITS and trnL-trnF + rbcL + atpB-rbcL analyses).The phylogenetic results, as well as presence of the stalactites in the outer cell walls of the testa and lack of the rosulate leaves, confirm the distinctive nature of Monolepisspathulata from all Blitum and, therefore, the recent combination Blitumspathulatum cannot be accepted. Indeed, the morphological and molecular distinctive nature of this species from all Dysphanieae supports its recognition as a new monotypic genus, named herein as Neomonolepis (type species: N.spathulata). The basionym name Monolepisspathulata is also lectotypified on a specimen currently lodged at GH. Finally, while Micromonolepispusilla is confirmed as belonging to the tribe Chenopodieae, its position is not fully resolved. As this monotypic genus is morphologically divergent from Chenopodium, it is retained as distinct but it is acknowledged that further work is required to confirm its status.

Phylogeny and diversification history of the large Neotropical genus Philodendron (Araceae): Accelerated speciation in a lineage dominated by epiphytes

PREMISE OF THE STUDY

Philodendron is a large genus of ~560 species and among the most conspicuous epiphytic components of Neotropical forests, yet its phylogenetic relationships, timing of divergence, and diversification history have remained unclear. We present a comprehensive phylogenetic study for Philodendron and investigate its diversification, including divergence-time estimates and diversification rate shift analyses.

METHODS

We performed the largest phylogenetic reconstruction for Philodendron to date, including 125 taxa with a combined dataset of three plastid regions (petD, rpl16, and trnK/matK). We estimated divergence times using Bayesian evolutionary analysis sampling trees and inferred shifts in diversification rates using Bayesian analysis of macroevolutionary mixtures.

KEY RESULTS

We found that Philodendron, its three subgenera, and the closely related genus Adelonema are monophyletic. Within Philodendron subgenus Philodendron, 12 statistically well-supported clades are recognized. The genus Philodendron originated ~25 mya and a diversification rate upshift was detected at the origin of subgenus Philodendron ~12 mya.

CONCLUSIONS

Philodendron is a species-rich Neotropical lineage that diverged from Adelonema during the late Oligocene. Within Philodendron, the three subgenera currently accepted are recovered in two lineages: one contains the subgenera Meconostigma and Pteromischum and the other contains subgenus Philodendron. The lineage containing subgenera Meconostigma and Pteromischum underwent a consistent diversification rate. By contrast, a diversification rate upshift occurred within subgenus Philodendron ~12 mya. This diversification rate upshift is associated with the species radiation of the most speciose subgenus within Philodendron. The sections accepted within subgenus Philodendron are not congruent with the clades recovered. Instead, the clades are geographically defined.

Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia

We present raw sequence reads and genome assemblies derived from 17 accessions of the Ethiopian orphan crop plant enset (Ensete ventricosum (Welw.) Cheesman) using the Illumina HiSeq and MiSeq platforms. Also presented is a catalogue of single-nucleotide polymorphisms inferred from the sequence data at an average density of approximately one per kilobase of genomic DNA.

The use of the hypervariable P8 region of trnL(UAA) intron for identification of orchid species: Evidence from restriction site polymorphism analysis

The P8 stem-loop region of the trnL intron, which is known to be hypervariable in size with multiple repeat motifs and created difficulties in alignment, is always excluded in phylogenetic as well as barcode analyses. This region was investigated for species discrimination in 98 taxa of orchids belonging to the tribe Vandeae using in silico mapping of restriction site polymorphism. The length of the P8 regions varied from 200 nucleotides in Aerides rosea to 669 nucleotides in Dendrophylax sallei. Forty two taxa had unique lengths, while as many as eight shared a common length of 521 nucleotides. Of the 35 restriction endonucleases producing digestions in the P8 regions, three, viz., AgsI, ApoI and TspDTI turned out to have recognition sites across all the 98 taxa being studied. When their restriction data were combined, 92 taxa could be discriminated leaving three taxon pairs. However, Acampe papillosa and Aeranthes arachnites despite having similar restriction sites differed in their P8 lengths. This is the first report on thorough investigation of the P8 region of trnL intron for search of species specific restriction sites and hence its use as a potential plant DNA barcode.

Genetic diversity analysis of cultivated Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] populations from southwestern Ethiopia using inter simple sequence repeats (ISSR) marker

Background

Korarima (Aframomum corrorima) is a perennial and aromatic herb native and widely distributed in southwestern Ethiopia. It is known for its fine flavor as a spice in various Ethiopian traditional dishes. Few molecular studies have been performed on this species so far. In the present paper, the ISSR technique was employed to study the genetic diversity in populations of cultivated A. corrorima.

Results

Seven ISSR primers produced a total of 86 clearly scorable DNA bands. High levels of genetic diversity were detected in cultivated A. corrorima (percentage of polymorphic bands = 97.67%, gene diversity = 0.35, Shannon’s information index = 0.52). Analysis of molecular variance (AMOVA) showed that 27.47% of the variation is attributed to the variation among populations and 72.53% to the variation within populations. The F_st (0.28) value showed a significant (p < 0.0001) genetic differentiation among populations. This was supported by the high coefficient of gene differentiation (G_st = 0.32) and low estimated gene flow (Nm = 1.08). A neighbor-joining dendrogram showed that the thirteen cultivated populations were separated into three clusters, which was in good accordance with the results provided by the two dimensional and three dimensional coordinate analyses. However, the clusters did not reveal clear pattern of populations clustering according to their geographic origin. This could be due to human mediated transfer of genetic material among different localities.

Conclusion

The genetic diversity in populations of A. corrorima from the southwestern part of Ethiopia was relatively high. This finding should be taken into account when conservation actions, management policies for the species and site identification for in situ and ex situ conservation strategies are developed. Mizan Teferi II population displayed the highest genetic diversity; this population should be considered as the key site in designing conservation strategies for this crop. In addition, Jimma I and Jimma II populations with lowest genetic diversity, should also be considered due to the putative risk of extinction that they face because of the low genetic diversity.

Evaluating the Feasibility of Five Candidate DNA Barcoding Loci for Philippine Lasianthus Jack (Lasiantheae: Rubiaceae)

Introduction

The pantropical genus Lasianthus Jack is identified for high phenotypic plasticity making traditional taxonomic identification difficult. Having some members with important medicinal properties, a precise complimentary identification through DNA barcoding is needed for species delineation.

Materials and Methods

In this study, 12 samples representing six Philippine Lasianthus species were used to determine the most efficient barcoding loci among the cpDNA markers (matK, rbcL, rps16, and trnT-F) and nrDNA (ITS) based on the criteria of universality, discriminatory power, and resolution of species.

Results

The results revealed that ITS has the recommended primer universality, greatest interspecific divergences, and average resolution of species. Among the cpDNA markers, matK and rbcL are recommended but with minimal resolution of species. While trnT-F showed moderate interspecific variations and resolution of Lasianthus species, rps16 has the lowest interspecific divergence and resolution of species.

Conclusion

Consequently, ITS is the potential ideal DNA barcode for Lasianthus species.

SUMMARY

ITS, matK, and rps16 markers have the excellent amplification and sequence qualityITS marker has the highest interspecific divergence with the maximum values, followed by matK, rbcL, trnT-F, and rps16, respectivelyAll markers except rps16 yielded average resolution to Lasianthus speciesITS marker is the most ideal locus in terms of excellent universality, high interspecific discriminatory ability, and average species resolution. Abbreviations used: ITS: Internal Transcribe Spacer, matK: maturase K, rbcL: ribulose-1,5-biphospahte-carboxylase, rps16: ribosomal protein 16 small subunit gene.

Choosing and Using Introns in Molecular Phylogenetics

Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.

Filogenia de los cánidos actuales (Carnivora: Canidae) mediante análisis de congruencia de caracteres bajo parsimonia

Las relaciones de parentesco entre los cánidos recientes han sido conflictivas. Entre los problemas más notables se tienen la monofilia del clado de los lobos por un lado y la de los cánidos suramericanos por el otro, así como las posiciones filogenéticas de Nyctereutes, Urocyon, Otocyon, Chrysocyon, Speothos y Lycaon. En este trabajo analizamos las relaciones filogenéticas de las 35 especies de cánidos recientes mediante análisis de congruencia de caracteres bajo máxima parsimonia utilizando datos morfológicos, moleculares, citogenéticos, de historia de vida, ecológicos y comportamentales. Con el objeto de reconocer el aporte de cada matriz y evaluar su combinabilidad, realizamos análisis de congruencia taxonómica entre particiones. No se detectaron incongruencias duras entre las particiones, lo que nos permitió realizar un análisis combinado sin alteraciones sobre la matriz. La topología resultante sugiere que Nyctereutes radia temprano en la historia de la subfamilia Caninae, mientras que el resto de taxones se agrupan en tres clados: zorros rojos, lobos y cánidos suramericanos. Se corrobora la monofilia de los géneros Urocyon, Lycalopex y Vulpes, pero no la de Canis. Los taxones Urocyon y Otocyon son grupos hermanos y quedan ubicados en la base del clado de los zorros rojos (Vulpini). Las especies de Vulpes quedan organizadas en términos biogeográficos con dos clados hermanos, uno conformado por las especies holárticas y el otro por las especies afrotropicales e indomalayas. La evolución de los cánidos suramericanos presenta una estructura de radiación jerárquica con el género Lycalopex en la parte terminal. El taxón Speothos forma un clado con los otros dos géneros monotípicos que poseen talón cortante (Lycaon y Cuon), lo que indica que esta adaptación a la hipercarnivoría evolucionó una sola vez en la historia de los Caninae.

Trap diversity and character evolution in carnivorous bladderworts (Utricularia, Lentibulariaceae)

Bladderworts (Utricularia, Lentibulariaceae, Lamiales) constitute the largest genus of carnivorous plants but only aquatic species (about one fifth of the genus) have so far been thoroughly studied as to their suction trap functioning. In this study, we comparatively investigated trap biomechanics in 19 Utricularia species to examine correlations between life-forms, trapping mechanisms, and functional-morphological traits. Our investigations show the existence of two functional trap principles (passive trap in U. multifida vs. active suction traps), and - in active suction traps - three main trapdoor movement types (with several subtypes). The trapdoor movement types and their corresponding functional-morphological features most presumably represent adaptations to the respective habitat. We furthermore give insights into fluid dynamics during suction in three representatives of the main types of trapdoor movement. The results on functional morphology and trapdoor movement were mapped onto a new phylogenetic reconstruction of the genus, derived from the rapidly evolving chloroplast regions trnK, rps16 and trnQ-rps16 and a sampling of 105 Utricularia species in total. We discuss potential scenarios of trap character evolution and species radiation, highlighting possible key innovations that enable such a unique carnivorous lifestyle in different habitats.

Genetic structure and relationships within and between cultivated and wild korarima [Aframomum corrorima (Braun) P.C.M. Jansen] in Ethiopia as revealed by simple sequence repeat (SSR) markers

BACKGROUND

Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a spice crop native to Ethiopia. Understanding the extent and partitioning of diversity within and among crop landraces and their wild relatives is among the first steps in conserving and measuring their genetic potential. The present study is aimed at characterizing the population genetic structure and relationships between cultivated and wild korarima in the southwestern part of Ethiopia.

RESULTS

We analyzed a total of 195 individuals representing seven wild and fourteen cultivated populations. Eleven polymorphic simple sequence repeat (SSR) markers were used. We observed a total of 53 alleles across the eleven loci and individuals. In total, 32 alleles were detected in the cultivated populations, whereas 49 alleles were detected in the wild populations. We found higher genetic diversity in wild populations than in the cultivated counterpart. This result implies the potential of wild korarima as a possible source for novel alleles contributing to the improvement of cultivated korarima. Analysis of molecular variance (AMOVA) showed significant but low differentiation between cultivated and wild korarima populations. Similarly, neighbour-joining and STRUCTURE analyses did not group cultivated and wild populations into two distinct clusters. The lack of clear differentiation between cultivated and wild populations could be explained by historical and contemporary gene flow between the two gene pools.

CONCLUSION

The 11 SSR loci developed in this study could be employed to examine genetic diversity and population structure of korarima in other countries as well as other Aframomum species. From the five administrative zones considered in this study, the Bench-Magi and Sheka zone showed populations with high genetic diversity, and these populations could be used as a potential starting point for in-situ and ex-situ germplasm conservation and korarima improvement through breeding programs after proper agronomic evaluation.

No evidence of contemporary interploidy gene flow between the closely related European woodland violets Viola reichenbachiana and V. riviniana (sect. Viola, Violaceae)

Viola reichenbachiana (2n = 4x = 20) and V. riviniana (2n = 8x = 40) are closely related species widely distributed in Europe, often sharing the same habitat throughout their overlapping ranges. It has been suggested in numerous studies that their high intraspecific morphological variability and plasticity might have been further increased by interspecific hybridisation in contact zones, given the sympatry of the species and the incomplete sterility of their hybrid. The aims of this study were to: (i) confirm that V. reichenbachiana and V. riviniana have one 4x genome in common, and (ii) determine the impact of hybridisation and introgression on genetic variation of these two species in selected European populations. For our study, we used 31 Viola populations from four European countries, which were analysed using AFLP and sequencing of a variable plastid intergenic spacer, trnH-psbA. Our analysis revealed that V. reichenbachiana exhibited larger haplotype diversity, having three species-specific haplotypes versus one in V. riviniana. The relationships among haplotypes suggest transfer of common haplotypes into V. riviniana from both V. reichenbachiana and hypothetically the other, now extinct, parental species. AFLP analysis showed low overall genetic diversity of both species, with V. riviniana showing higher among-population diversity. None of the morphologically designated hybrid populations had additive AFLP polymorphisms that would have indicated recent hybridisation. Also, kinship coefficients between both species did not indicate gene flow. V. riviniana showed significant population subdivision and significant isolation by distance, in contrast to V. reichenbachiana. The results indicate lack of gene flow between species, high influence of selfing on genetic variability, as well as probably only localised introgression toward V. riviniana.

The specific host plant DNA detection suggests a potential migration of Apolygus lucorum from cotton to mungbean fields

The polyphagous mirid bug Apolygus lucorum (Heteroptera: Miridae) has more than 200 species of host plants and is an insect pest of important agricultural crops, including cotton (Gossypium hirsutum) and mungbean (Vigna radiata). Previous field trials have shown that A. lucorum adults prefer mungbean to cotton plants, indicating the considerable potential of mungbean as a trap crop in cotton fields. However, direct evidence supporting the migration of A. lucorum adults from cotton to mungbean is lacking. We developed a DNA-based polymerase chain reaction (PCR) approach to reveal the movement of A. lucorum between neighboring mungbean and cotton fields. Two pairs of PCR primers specific to cotton or mungbean were designed to target the trnL-trnF region of chloroplast DNA. Significant differences in the detectability half-life (DS50) were observed between these two host plants, and the mean for cotton (8.26 h) was approximately two times longer than that of mungbean (4.38 h), requiring weighted mean calculations to compare the detectability of plant DNA in the guts of field-collected bugs. In field trials, cotton DNA was detected in the guts of the adult A. lucorum individuals collected in mungbean plots, and the cotton DNA detection rate decreased successively from 5 to 15 m away from the mungbean-cotton midline. In addition to the specific detection of cotton- and mungbean-fed bugs, both cotton and mungbean DNA were simultaneously detected within the guts of single individuals caught from mungbean fields. This study successfully established a tool for molecular gut-content analyses and clearly demonstrated the movement of A. lucorum adults from cotton to neighboring mungbean fields, providing new insights into understanding the feeding characteristics and landscape-level ecology of A. lucorum under natural conditions.

Pulling the sting out of nettle systematics - A comprehensive phylogeny of the genus Urtica L. (Urticaceae)

The genus Urtica L. is subcosmopolitan, found on all continents (except Antarctica) and most extratropical islands and ranges from Alaska to Patagonia, Spitzbergen to the Cape and Camtschatka to the subantarctic islands. However, throughout its geographical range morphologically nearly indistinguishable species are found alongside morphologically quite disparate species, with the overall diversity of morphological characters extremely limited. The systematics of Urtica have puzzled scientists for the past 200years and no single comprehensive attempt at understanding infrageneric relationships has been published in the past, nor are species delimitations unequivocally established. We here provide the first comprehensive phylogeny of the genus including 61 of the 63 species recognized, represented by 144 ingroup accessions and 14 outgroup taxa. The markers ITS1-5.8S-ITS2, psbA-trnH intergenic spacer, trnL-trnF and trnS-trnG are used. The phylogeny is well resolved. The eastern Asian Zhengyia shennongensis T. Deng, D.G. Zhang & H. Sun is retrieved as sister to Urtica. Within Urtica, a clade comprising the western Eurasian species U. pilulifera L. and U. neubaueri Chrtek is sister to all other species of the genus. The phylogenetic analyses retrieve numerous well-supported clades, suggesting previously unsuspected relationships and implying that classically used taxonomic characters such as leaf morphology and growth habit are highly homoplasious. Species delimitation is problematical, and several accessions assigned to Urtica dioica L. (as subspecies) are retrieved in widely different places in the phylogeny. The genus seems to have undergone numerous dispersal-establishment events both between continents and onto different islands. Three recent species radiations are inferred, one in America centered in the Andes, one in New Zealand, and one in northern Eurasia which includes Urtica dioica s.str. sensu Henning et al. (2014). The present study provides the basis of a critical re-examination of species limits and taxonomy, but also of the dispersal ecology of this widespread plant group and an in-depth study of the three clades with recent radiations.

Phylotranscriptomic Analysis Based on Coalescence was Less Influenced by the Evolving Rates and the Number of Genes: A Case Study in Ericales

Advances in high-throughput sequencing have generated a vast amount of transcriptomic data that are being increasingly used in phylogenetic reconstruction. However, processing the vast datasets for a huge number of genes and even identifying optimal analytical methodology are challenging. Through de novo sequenced and retrieved data from public databases, we identified 221 orthologous protein-coding genes to reconstruct the phylogeny of Ericales, an order characterized by rapid ancient radiation. Seven species representing different families in Ericales were used as in-groups. Both concatenation and coalescence methods yielded the same well-supported topology as previous studies, with only two nodes conflicting with previously reported relationships. The results revealed that a partitioning strategy could improve the traditional concatenation methodology. Rapidly evolving genes negatively affected the concatenation analysis, while slowly evolving genes slightly affected the coalescence analysis. The coalescence methods usually accommodated rate heterogeneity better and required fewer genes to yield well-supported topologies than the concatenation methods with both real and simulated data.

Detection of seed DNA in regurgitates of granivorous carabid beetles

Granivory can play a pivotal role in influencing regeneration, colonization as well as abundance and distribution of plants. Due to their high abundance, nutrient content and longevity, seeds are an important food source for many animals. Among insects, carabid beetles consume substantial numbers of seeds and are thought to be responsible for a significant amount of seed loss. However, the processes that govern which seeds are eaten and are therefore prevented from entering the seedbank are poorly understood. Here, we assess if DNA-based diet analysis allows tracking the consumption of seeds by carabids. Adult individuals of Harpalus rufipes were fed with seeds of Taraxacum officinale and Lolium perenne allowing them to digest for up to 3 days. Regurgitates were tested for the DNA of ingested seeds at eight different time points post-feeding using general and species-specific plant primers. The detection of seed DNA decreased with digestion time for both seed species, albeit in a species-specific manner. Significant differences in overall DNA detection rates were found with the general plant primers but not with the species-specific primers. This can have implications for the interpretation of trophic data derived from next-generation sequencing, which is based on the application of general primers. Our findings demonstrate that seed predation by carabids can be tracked, molecularly, on a species-specific level, providing a new way to unravel the mechanisms underlying in-field diet choice in granivores.

Stereoisomeric Composition of Natural Myrtucommulone A

Myrtucommulone A (MC A) (1), isolated from Myrtus communis (myrtle), shows the same pharmacological activity for inhibition of inflammation and induction of apoptosis as synthetic MC A, which consists of three stereoisomers, i.e., two enantiomers and one meso form. This led to the question of whether the natural MC A is a pure stereoisomer or a mixture of stereoisomers. The specific rotation and electronic circular dichroism (ECD) data of natural MC A (1) as well as of a pentacyclic derivative 4 revealed that naturally occurring MC A (1) consists of the racemate and the meso form in a 1:1 ratio. A probable precursor of MC A (1), nor-semimyrtucommulone (5), was also isolated from myrtle as a racemate. The absolute configurations of the enantiomers of 1 and 5 were determined using a combination of experimental and quantum-chemical calculated ECD spectra.

Intercontinental long-distance dispersal of Canellaceae from the New to the Old World revealed by a nuclear single copy gene and chloroplast loci

Canellales, a clade consisting of Winteraceae and Canellaceae, represent the smallest order of magnoliid angiosperms. The clade shows a broad distribution throughout the Southern Hemisphere, across a diverse range of dry to wet tropical forests. In contrast to their sister-group, Winteraceae, the phylogenetic relations and biogeography within Canellaceae remain poorly studied. Here we present the phylogenetic relationships of all currently recognized genera of Canellales with a special focus on the Old World Canellaceae using a combined dataset consisting of the chloroplast trnK-matK-trnK-psbA and the nuclear single copy gene mag1 (Maigo 1). Within Canellaceae we found high statistical support for the monophyly of Warburgia and Cinnamosma. However, we also found relationships that differ from previous studies. Cinnamodendron splitted into two clades, a South American clade and a second clade confined to the Antilles and adjacent areas. Cinnamodendron from the Antilles, as well as Capsicodendron, South American Cinnamodendron and Pleodendron were not monophyletic. Consequently, Capsicodendron should be included in the South American Cinnamodendron clade and the genus Pleodendron merged with the Cinnamodendron clade from the Antilles. We also found that Warburgia (restricted to mainland eastern Africa) together with the South American Cinnamodendron and Capsicodendron are sister to the Malagasy genus Cinnamosma. In addition to the unexpected geographical relationships, both biogeographic and molecular clock analyses suggest vicariance, extinction, and at least one intercontinental long-distance-dispersal event. Our dating result contrasts previous work on Winteraceae. Diversification of Winteraceae took place in the Paleocene, predating the Canellaceae diversification by 13 MA in the Eocene. The phylogenetic relationships for Canellaceae supported here offer a solid framework for a future taxonomic revision of the Canellaceae.

A new angiosperm from the Crato Formation (Araripe Basin, Brazil) and comments on the Early Cretaceous Monocotyledons

The Crato Formation paleoflora is one of the few equatorial floras of the Early Cretaceous. It is diverse, with many angiosperms, especially representatives of the clades magnoliids, monocotyledons and eudicots, which confirms the assumption that angiosperm diversity during the last part of the Early Cretaceous was reasonably high. The morphology of a new fossil monocot is studied and compared to all other Smilacaceae genus, especially in the venation. Cratosmilax jacksoni gen. et sp. nov. can be related to the Smilacaceae family, becoming the oldest record of the family so far. Cratosmilax jacksoni is a single mesophilic leaf with entire margins, ovate shape, with acute apex and base, four venation orders and main acrodromous veins. It is the first terrestrial monocot described for the Crato Formation, monocots were previously described for the same formation, and are considered aquatics. Cratosmilax jacksoni is the first fossil record of Smilacaceae in Brazil, and the oldest record of this family.

Chloroplast DNA sequence utility for the lowest phylogenetic and phylogeographic inferences in angiosperms: the tortoise and the hare IV

PREMISE OF THE STUDY

Noncoding chloroplast DNA (NC-cpDNA) sequences are the staple data source of low-level phylogeographic and phylogenetic studies of angiosperms. We followed up on previous papers (tortoise and hare II and III) that sought to identify the most consistently variable regions of NC-cpDNA. We used an exhaustive literature review and newly available whole plastome data to assess applicability of previous conclusions at low taxonomic levels.

METHODS

We aligned complete plastomes of 25 species pairs from across angiosperms, comparing the number of genetic differences found in 107 NC-cpDNA regions and matK. We surveyed Web of Science for the plant phylogeographic literature between 2007 and 2013 to assess how NC-cpDNA has been used at the intraspecific level.

KEY RESULTS

Several regions are consistently the most variable across angiosperm lineages: ndhF-rpl32, rpl32-trnL((UAG)), ndhC-trnV((UAC)), 5'rps16-trnQ((UUG)), psbE-petL, trnT((GGU))-psbD, petA-psbJ, and rpl16 intron. However, there is no universally best region. The average number of regions applied to low-level studies is ∼2.5, which may be too little to access the full discriminating power of this genome.

CONCLUSIONS

Plastome sequences have been used successfully at lower and lower taxonomic levels. Our findings corroborate earlier works, suggesting that there are regions that are most likely to be the most variable. However, while NC-cpDNA sequences are commonly used in plant phylogeographic studies, few of the most variable regions are applied in that context. Furthermore, it appears that in most studies too few NC-cpDNAs are used to access the discriminating power of the cpDNA genome.

Analysis of variation in chloroplast DNA sequences

This chapter introduces and reviews methods for analyzing variation in chloroplast DNA, mainly by polymerase chain reaction (PCR) and subsequent revelation of polymorphisms. Sources for chloroplast primers are discussed, as well as methods such as Sanger sequencing, PCR followed by restriction fragment length polymorphism (RFLP), gel electrophoresis, fragment analysis on automated DNA sequencers, denaturing high-performance liquid chromatography (dHPLC), and next-generation sequencing (NGS). A special section deals with peculiarities of chloroplast DNA variation, such as tandem repeats and mini- and microsatellites.