Recent Molecular-based Studies Research Articles

The developmental hourglass model and recapitulation: An attempt to integrate the two models

Recapitulation is a hypothetical concept that assumes embryogenesis of an animal parallels its own phylogenetic history, sequentially developing from more ancestral features to more derived ones. This concept predicts that the earliest developmental stage of various animals should represent the most evolutionarily conserved patterns. Recent transcriptome‐based studies, on the other hand, have reported that mid‐embryonic, organogenetic periods show the highest level of conservation (the developmental hourglass model). This, however, does not rule out the possibility that recapitulation would still be detected after the mid‐embryonic period. In accordance with this, recapitulation‐like morphological features are enriched in late developmental stages. Moreover, our recent chromatin accessibility‐based study provided molecular evidence for recapitulation in the mid‐to‐late embryogenesis of vertebrates, as newly evolved gene regulatory elements tended to be activated at late embryonic stages. In this review, we revisit the recapitulation hypothesis, together with recent molecular‐based studies that support the developmental hourglass model. We contend that the recapitulation hypothesis does not entirely contradict the developmental hourglass model and that these two may even coexist in later embryonic stages of vertebrates. Finally, we review possible mechanisms underlying the recapitulation pattern of chromatin accessibility together with the hourglass‐like evolutionary conservation in vertebrate embryogenesis.

Ecological niche divergence contributes species differentiation in worm lizards (Blanus sp.) (Squamata: Amphisbaenia: Blanidae) in Mediterranean part of Anatolian peninsula and the Levantine region

The genus Blanus Wagler, 1830 (Squamata, Amphisbaenia) contains seven fossorial species found in the East Mediterranean Basin. Recent molecular-based studies suggested that former B. strauchi (Turkish worm lizard) is divided into three species spread from Southern Anatolia to Levantine region: B. strauchi, B. aporus and B. alexandri. Although these species not only have highly similar morphological characters but also are genetically distinct, the ecological niche differentiations have not been studied yet. We aim to predict the suitable habitats for related Blanus species and to determine niche overlaps and niche differentiation by similarity and identity tests. The occurrence records were obtained from literature and our own field surveys. These occurrence locations were assessed in 30 arc-second resolution layer, compatible with bioclimatic parameters from World-Clim ( www.worldclim.org ). Suitable habitat prediction analyses were performed in MaxEnt and the pairwise niche overlap comparisons were made in ENMTools. Our results show that precipitation and temperature dynamics may have an influence on the vegetation types, which provide suitable habitats for these species. Even in the most conservative model, where B.strauchi was designated as the ancestral species, the predicted distribution area was larger than the actual one. The niche overlap analysis confirms that the ecological differentiations among these taxa are valid. This result is in agreement with a previous molecular-based study. We speculate that the Messinian Salinity Crisis had an effect on precipitation and temperature dynamics and niche differentiation among the worm lizards, potentially contributing to species formation.

Examining the Evidence for an Adult Healthy Middle Ear Microbiome.

Otitis media (OM) is a cluster of diseases of the middle ear that commonly result from bacterial infection. OM subtypes in which the tympanic membrane is intact (acute otitis media and otitis media with effusion) are presumed to result from pathogen translocation through the eustachian tube. Recent molecular-based studies have suggested that a diverse middle ear microbiome exists in the absence of disease. These have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. Middle ear (ME), nasopharynx (NP), and external ear canal (EC) swabs were collected from a total of 25 adult patients undergoing cochlear implant, stapedotomy, or translabyrinthine vestibular schwannoma resection. Diagnostic culture, microscopy, quantitative PCR, and 16S rRNA gene amplicon sequencing were used to assess sample bacterial content. EC and NP microbiota were consistent with previous reports. In contrast, bacterial levels in ME samples were not significantly above those in unused control swabs. Commonly detected taxa were among recognized sequencing contaminants (Methylobacterium, Pseudomonas, and Acinetobacter). Linear regression of dominant ME taxa confirmed a negative relationship between relative abundance and bacterial load, consistent with contamination. No bacteria were detected by microscopy or diagnostic culture in any middle ear sample. Our findings cast substantial doubt on previous reports identifying a healthy middle ear microbiome using 16S amplicon sequencing.IMPORTANCE Recent molecular-based studies have suggested that a diverse middle ear microbiome in adults and children can exist in the absence of disease. These studies have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. While 16S rRNA gene amplicon sequencing has proven to be a highly informative technique in many clinical contexts, it is susceptible to spurious signal arising from sequencing reagent contaminants where sample biomass is low. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. In finding no evidence of viable bacterial cells in middle ear samples, our study further underlines the importance of careful consideration of amplicon sequence data derived from very-low-biomass contexts and the value of analytical approaches that combine culture and molecular techniques.

Epithemia hirudiniformis and Related Taxa within the Subgenus Rhopalodiella subg. nov. in Comparison to Epithemia subg. Rhopalodia stat nov. (Bacillariophyceae) from East Africa

Epithemia hirudiniformis and three morphologically related taxa, described in Rhopalodia by O. Muller from material collected in East Africa at the end of the 19th and the beginning of the 20th century were re-evaluated and lectotypes designated. Rhopalodiella as a new subgenus is proposed which refines O. Muller's infrageneric classification and to which all these taxa belong. In addition, the type of Epithemia rhopala, described by Ehrenberg from Egypt, was studied to examine the assumed synonymy, introduced by Hustedt, with some of Muller's species. This study, using light and scanning electron microscopy, was not only based on historic material but also more recent material from Africa, including samples from the Island of Reunion from which the new species Epithemia vandevijveri is described. The distribution of Epithemia subg. Rhopalodiella, known to be restricted to tropical Africa, is discussed based on literature data and own observations. Corresponding to recent molecular-based studies, Rhopalodia is given a new status as subgenus.

Hydrolithon braganum sp. nov. (Corallinaceae, Rhodophyta), the first known exclusively fossil semi-endophytic coralline red alga

Woelkerling W.J., Bassi D. and Iryu Y. 2012. Hydrolithon braganum sp. nov. (Corallinaceae, Rhodophyta), the first known exclusively fossil semi-endophytic coralline red alga. Phycologia 51: 604–611. DOI: 10.2216/11-119.1Hydrolithon braganum sp. nov., the first known exclusively fossil semi-endophytic species of Corallinaceae (Corallinales, Rhodophyta), is based on material from Integrated Ocean Drilling Program Expedition 310 cores of last deglacial age [c. 20,000–10,000 years before present] from reef terraces around Tahiti, French Polynesia. A detailed morphological–anatomical account is provided and morphological–anatomical similarities to other species are discussed. The taxonomic position of H. braganum is problematic in relation to recent proposals for changes to the circumscription of Hydrolithon. Evidence is presented to show that the morphological–anatomical criteria proposed in recent molecular-based studies are untenable for circumscribing genera called Hydrolithon and Porolithon. Thus, pending further research, the two genera are best treated as the Hydrolithon–Porolithon complex with Hydrolithon having nomenclatural priority, being polyphyletic, and encompassing one or several cryptic genera distinguishable on presently known molecular criteria but not distinguishable using presently known morphological–anatomical criteria.

Fire-adapted Gondwanan Angiosperm floras evolved in the Cretaceous

BackgroundFires have been widespread over the last 250 million years, peaking 60−125 million years ago (Ma), and might therefore have played a key role in the evolution of Angiosperms. Yet it is commonly believed that fireprone communities existed only after the global climate became more arid and seasonal 15 Ma. Recent molecular-based studies point to much earlier origins of fireprone Angiosperm floras in Australia and South Africa (to 60 Ma, Paleocene) but even these were constrained by the ages of the clades examined.ResultsUsing a molecular-dated phylogeny for the great Gondwanan family Proteaceae, with a 113-million-year evolutionary history, we show that the ancestors of many of its characteristic sclerophyll genera, such as Protea, Conospermum, Leucadendron, Petrophile, Adenanthos and Leucospermum (all subfamily Proteoideae), occurred in fireprone habitats from 88 Ma (83−94, 95% HPD, Mid-Upper Cretaceous). This coincided with the highest atmospheric oxygen (combustibility) levels experienced over the past 150 million years. Migration from non-fireprone (essentially rainforest-climate-type) environments was accompanied by the evolution of highly speciose clades with a range of seed storage traits and fire-cued seed release or germination mechanisms that was diagnostic for each clade by 71 Ma, though the ant-dispersed lineage (as a soil seed-storage subclade) was delayed until 45 Ma.ConclusionsFocusing on the widespread 113-million-year-old family Proteaceae, fireproneness among Gondwanan Angiosperm floras can now be traced back almost 90 million years into the fiery Cretaceous. The associated evolution of on-plant (serotiny) and soil seed storage, and later ant dispersal, affirms them as ancient adaptations to fire among flowering plants.

Taxonomy, skull diversity and evolution in a species complex of Myotis (Chiroptera: Vespertilionidae): a geometric morphometric appraisal

Phylogenetic relationships between taxa are not necessarily reflected by morphological data due to widespread homoplasy and convergence. However, combining morphological and molecular data provides insights into the evolution of biological forms and into the potential factors involved. Here we focus on a complex of three taxa of bats with unclear taxonomic affinities: Myotis myotis, Myotis blythii and Myotis punicus. Traditional morphometric methods failed to separate them, whereas recent molecular-based studies suggested that they constitute separate biological species. In the present study, landmark-based geometric morphometrics methods have been used to analyse the skull variability of 218 specimens belonging to this species complex. Patterns of size and shape delimitate three morphological groups that are congruent with the proposed taxonomic assignments, and therefore support species rank for all three major groups. These morphometrics results, however, suggest that M. myotis and M. punicus share shape characteristics in the rostrum and in the posterior part of the skull that differ from M. blythii. Because previous molecular phylogenetic analyses suggested that M. myotis and M. blythii are sister species, we interpret the similitude in skull morphology between M. myotis and M. punicus as a convergence probably related to their similar feeding habits. Within the taxon M. punicus, the skull of Corsican and Sardinian populations significantly differs from that of Maghrebian ones, suggesting the existence of further cryptic taxonomic diversity.

Current molecular aspects of the carcinogenesis of the uterine endometrium

Carcinogenesis in many tissues is a multistep process accompanied by a variety of morphologic, biochemical, and genetic changes in each step. It is well known that endometrial cancers arise through a series of precursor lesions, simple, complex, and atypical hyperplasia, by unopposed and prolonged estrogen stimulation. It is also accepted that there is an estrogen-independent type in which the precursor lesions are not identified. Recent molecular-based evidence has revealed three possible pathways for endometrial carcinogenesis, namely hyperplasia, metaplasia, and de novo pathways. The pathways each have their own features in both histopathology and molecular biology. Such understanding of the molecular profile of endometrial carcinoma prompted us to revise the classic criteria in histopathology regarding endometrial carcinogenesis. The recent molecular-based studies have provided a concept of endometrial intraepithelial lesions: endometrial intraepithelial neoplasia (EIN) as the precursor lesions of endometrial carcinomas. The new terminology might improve cancer screening protocols and treatment modalities.

Current molecular aspects of the carcinogenesis of the uterine endometrium

Carcinogenesis in many tissues is a multistep process accompanied by a variety of morphologic, biochemical, and genetic changes in each step. It is well known that endometrial cancers arise through a series of precursor lesions, simple, complex, and atypical hyperplasia, by unopposed and prolonged estrogen stimulation. It is also accepted that there is an estrogen-independent type in which the precursor lesions are not identified. Recent molecular-based evidence has revealed three possible pathways for endometrial carcinogenesis, namely hyperplasia, metaplasia, and de novo pathways. The pathways each have their own features in both histopathology and molecular biology. Such understanding of the molecular profile of endometrial carcinoma prompted us to revise the classic criteria in histopathology regarding endometrial carcinogenesis. The recent molecular-based studies have provided a concept of endometrial intraepithelial lesions: endometrial intraepithelial neoplasia (EIN) as the precursor lesions of endometrial carcinomas. The new terminology might improve cancer screening protocols and treatment modalities.