A checklist for choosing between R packages in ecology and evolution

1. The open source and free programming language R is a phenomenal mechanism to address a multiplicity of challenges in ecology and evolution. It is also a complex ecosystem because of the diversity of solutions available to the analyst.
2. Packages for R enhance and specialize the capacity to explore both niche data/experiments and more common needs. However, the paradox of choice or how we select between many seemingly similar options can be overwhelming and lead to different potential outcomes.
3. There is extensive choice in ecology and evolution between packages for both fundamental statistics and for more specialized domain‐level analyses.
4. Here, we provide a checklist to inform these decisions based on the principles of resilience, need, and integration with scientific workflows for evidence.
5. It is important to explore choices in any analytical coding environment—not just R—for solutions to challenges in ecology and evolution, and document this process because it advances reproducible science, promotes a deeper understand of the scientific evidence, and ensures that the outcomes are correct, representative, and robust.

     

PxdA interacts with the DipA phosphatase to regulate peroxisome hitchhiking on early endosomes

In canonical microtubule-based transport, adaptor proteins link cargoes to dynein and kinesin motors. Recently, an alternative mode of transport known as “hitchhiking” was discovered, where cargoes achieve motility by hitching a ride on already-motile cargoes, rather than attaching to a motor protein. Hitchhiking has been best studied in two filamentous fungi, Aspergillus nidulans and Ustilago maydis. In U. maydis, ribonucleoprotein complexes, peroxisomes, lipid droplets (LDs), and endoplasmic reticulum hitchhike on early endosomes (EEs). In A. nidulans, peroxisomes hitchhike using a putative molecular linker, peroxisome distribution mutant A (PxdA), which associates with EEs. However, whether other organelles use PxdA to hitchhike on EEs is unclear, as are the molecular mechanisms that regulate hitchhiking. Here we find that the proper distribution of LDs, mitochondria, and preautophagosomes do not require PxdA, suggesting that PxdA is a peroxisome-specific molecular linker. We identify two new pxdA alleles, including a point mutation (R2044P) that disrupts PxdA’s ability to associate with EEs and reduces peroxisome movement. We also identify a novel regulator of peroxisome hitchhiking, the phosphatase DipA. DipA colocalizes with EEs and its association with EEs relies on PxdA. Together, our data suggest that PxdA and the DipA phosphatase are specific regulators of peroxisome hitchhiking on EEs.     

Contact relations and guidance of primordial germ cells on their migratory route in embryos of Xenopus laevis

This paper describes the relationship between primordial germ cells (p.g.cs) and the substrate over which they migrate in early embryos of the anuran amphibian Xenopus laevis. P.g.cs migrate from the embryonic gut to the dorsal body wall along the dorsal mesentery at the earliest swimming stage. Our earlier papers have described the way in which p.g.cs move in vitro. In this work we have studied the shape and cytoarchitecture of both p.g.cs and the coelomic epithelial cells (c.e.cs) over which they migrate. We have concentrated on three aspects of the morphology of these cells: first the shapes of the c.e.cs and the way that they affect the shapes of the p.g.cs; secondly the presence of adhesion plaques between the two types of cell; and thirdly the arrangement of cytoskeleton elements. The results show that c.e.cs in the dorsal mesentery are orientated cranio-caudally while those on the dorsal body wall and at the junction with the mesentery are arranged transversely, at 90 degrees to the cranio-caudal plane. P.g.cs are found in both elongated and rounded state. Where elongated, they are always in the same plane as the c.e.cs with which they are associated. The implications of this are discussed. Adhesion plaques between p.g.cs and c.e.cs are shown both by disaggregation studies and transmission electron microscope studies. Plaques are associated with the well defined microfilamentous cytoskeleton of c.e.cs, but only with a sparse array of filaments in p.g.cs. The only parts of p.g.cs where filaments are regularly found are their filopodia, which are generally seen on elongated p.g.cs in longitudinal section. We suggest on the basis of this work that p.g.cs have a dispersed cytoskeleton except during filopod extension, that they move by forming direct adhesion plaques with c.e.cs, and that c.e.cs provide a firm orientated support and possible guide to p.g.c. movement.     

Insect parasites of the winter moth,Operophtera brumata (L.) (Lepidoptera: Geometridae) in western Europe

Summary Sixty-three species of insect parasites of the winter moth,Operophtera brumata (L.) (Lepidoptera: Geometridae), including 26 reared in the present investigation and 37 recorded only in the literature, are listed. Eleven of those reared in the present study are new parasite records for winter moth. Thirteen of the records from the literature are questionable because in each case the identity of either the parasite or host in uncertain. Notes on distribution and life-history are given for species reared in the present study.

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Zusammenfassung In vorliegender Untersuchung wurden insgesamt 63 Insekten als Parasiten des Frostspanner,Operophtera brumata (L.), behandelt. Von diesen sind 37 Arten nur aus der Literatur bekannt. Die übrigen 26 Arten wurden aus dem gesammelten Material gezüchtet. Von letzteren waren 11 Arten bis jetzt noch nicht als Parasiten der Frostspanner bekannt. 13 in der Literatur genannte Arten sind mit einem Fragezeichen zu versehen, weil die Bestimmung der Parasiten-Arten oder des Wirtes zweifelhaft erscheint. Bemerkungen über die Biologie und Verbreitung der von uns gezüchteten Arten werden gegeben.