A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

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Giant clams discriminate threats along a risk gradient and display varying habituation rates to different stimuli

It is often beneficial for animals to discriminate between different threats and to habituate to repeated exposures of benign stimuli. While much is known about risk perception in vertebrates and some invertebrates, risk perception in marine invertebrates is less extensively studied. One method to study risk perception is to habituate animals to a series of exposures to one stimulus, and then present a novel stimulus to test if it transfers habituation. Transfer of habituation is seen as a continued decrease in response while lack of transfer is seen either by having a similar or greater magnitude response. We asked whether giant clams (Tridacna maxima) discriminate between biologically relevant types of threats along a risk gradient. Giant clams retract their mantle and close their shell upon detecting a threat. While closed, they neither feed nor photosynthesize, and prior work has shown that the cost of being closed increases as the duration of their response increases. We recorded a clam's latency to emerge after simulated threats chosen to represent a risk gradient: exposure to a small shading event, a medium shading event, a large shading event (chosen to simulate fish swimming above them), tapping on their shell and touching their mantle (chosen to simulate different degrees of direct attack). Although these stimuli are initially perceived as threatening, we expected clams to habituate to them because they are ultimately non‐damaging and it would be costly for clams to remain closed for extended periods of time when there is no threat present. Clams had different initial latencies to emerge and different habituation rates to these treatments, and they did not transfer habituation to higher risk stimuli and to some lower risk stimuli. These results suggest that clams discriminated between these stimuli along a risk gradient and the lack of habituation transfer shows that the new stimulus was perceived as a potential threat. This study demonstrates that sessile bivalves can discern between levels of predatory threat. These photosynthetic clams may benefit from being able to categorize predator cues for efficient energy allocation.     

Price of disorder in the lac repressor hinge helix

The Lac system of genes has been pivotal in understanding gene regulation. When the lac repressor protein binds to the correct DNA sequence, the hinge region of the protein goes through a disorder to order transition. The structure of this region of the protein is well understood when it is in this bound conformation, but less so when it is not. Structural studies show that this region is flexible. Our simulations show this region is extremely flexible in solution; however, a high concentration of salt can help kinetically trap the hinge helix. Thermodynamically, disorder is more favorable without the DNA present.     

三突起类花粉形态学及其度量和描述

三突起类(Triprojectacites Mtchedlishvili,1961 emend. Stanley,1970)是晚白垩世—古新世北半球广泛分布的一类被子植物花粉,具有重要的孢粉植物分区和地层意义。其主要特征是发育突出于体的突起和其末端的沟状萌发器。由于形态复杂多变,该类花粉在度量和描述中存在不少难点,缺少明确而统一的标准,制约了其分类的进展。本文根据对松辽盆地白垩系三突起类标本的萌发器、极性、突起形态和纹饰等分类性状的观察,结合对前人在三突起类描述、分类中存在问题的剖析,提出了一套形态学术语、度量方法和参数。它们不仅能有效避免各种误差、准确反映和描述三突起类花粉的形态特征,而且还适用于不同位置保存的标本,有助于建立这些标本之间的联系,为三突起类花粉分类系统提供了科学合理的形态学度量和描述基础。     

Pollen morphology of Trigonostemon and its relatives (Euphorbiaceae)

The pollen of Trigonostemon and the related genera Dimorphocalyx, Ostodes, Tritaxis and Jatropha (outgroup) has been studied with light microscopy, and scanning and transmission electron microscopy. The two major pollen types within Trigonostemon correlate well with macromorphological characters. Species belonging to the Trigonostemon reidioides type have pollen with ‘croton pattern’ ornamentation, a pistil with deeply divided stigmas (to at least half the length of the stigma arm) and stamens with a protruding appendage on the connective, while species of the Trigonostemon verrucosus type have verrucate (to almost gemmate) pollen, stigmas that are shortly cleft and stamens without an appendage on the connective. Dimorphocalyx, Ostodes, Tritaxis and Jatropha (outgroup) have similar pollen morphology, while Trigonostemon deviates from these genera in the absence of the ‘vertically’ striate ornamentation on the subunits. Therefore, when compared with an existing phylogeny of the Euphorbiaceae, the pollen characters of Trigonostemon appear to be derived. Moreover, because the ‘croton pattern’ ornamentation itself is widely shared by the ‘inaperturate crotonoids’, the loss of that structure in the Trigonostemon verrucosus type pollen is considered a further apomorphy.     

Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata

Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species (‘common GO’) within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.     

玉兰新分类系统的研究

作者对多年来采集的玉兰植物标本进行了分类、整理和研究。结果表明,玉兰是个野生和栽培兼有、形态多样性的复合型种群,并首次提出玉兰种下新分类系统。该新系统是：种—亚种—变种,其中包括2亚种(1新组合亚种)、6变种(1新变种和3新改隶组合变种)。为进一步深入开展玉兰形变理论、新品种选育和开发利用等研究提供了科学依据。     

The cephalopod macrosystem: A historical review, the present state of knowledge, and unsolved problems: 3. Classification of Bactritoidea and Ammonoidea

A new classification is proposed in which Bactritoidea and Ammonoidea are considered as subclasses. The subclass Bactritoidea includes a single order, Bactritida. The subclass Ammonoidea includes ten orders: Anarcestida (suborders Agoniatitina, Auguritina, Anarcestina, Gephurocerina, Timanocerina, and Prolecanitina), Tornocerida, Goniatitida (with suborders Goniatitina and Cyclolobina), Praeglyphiocerida, Clymeniida (with suborders Gonioclymeniina and Clymeniina), Medlicottiida, Ceratitida (with suborders Paraceltitina, Otocerina, Meekocerina, Sagecerina, Ptychitina, Ceratitina, Pinacocerina, Megaphyllitina, Arcestina, and Lobitina), Phyllocerida, Lytocerida (with suborders Lytocerina and Turrilitina), and Ammonitida (with suborders Psilocerina, Haplocerina, Stephanocerina, Cardiocerina, and Ancylocerina).     

The cephalopod macrosystem: A historical review, the present state of knowledge, and unsolved problems: 2. Classification of nautiloid cephalopods

Major classifications of nautiloid cephalopods are critically reviewed. It is suggested that this cephalopod group is subdivided into 5 subclasses and 17 orders: Ellesmeroceratoidea (including the orders Plectronocerida, Protactinocerida, Yanhecerida, and Ellesmerocerida), Endoceratoidea (including the orders Endocerida and Intejocerida), Actinoceratoidea (including the order Actinocerida), Nautiloidea (with the orders Basslerocerida, Tarphycerida, Lituitida, Discosorida, Oncocerida, and Nautilida), and Orthoceratoidea (including the orders Orthocerida, Ascocerida, Dissidocerida, and Bajkalocerida). The above orders are briefly described.