To minimize foraging time,use high‐efficiency,energy‐expensive search and capture methods when food is abundant but low‐efficiency,low‐cost methods during food shortages

Based on a mathematical model, I show that the amount of food in the habitat determines which among alternative methods for search of prey, respectively, for pursuit‐and‐capture give the shortest daily foraging time. The higher the locomotor activity, the higher the rate of energy expenditure and the larger the habitat space a predator can search for prey per time unit. Therefore, I assume that the more efficient a foraging method is, the higher its rate of energy expenditure. Survival selection favors individuals that use foraging methods that cover their energy needs in the shortest possible time. Therefore, I take the optimization criterion to be minimization of the daily foraging time or, equivalently, maximization of the rate of net energy gain. When time is limiting and food is in short supply, as during food bottleneck periods, low‐efficiency, low‐cost foraging methods give shorter daily foraging times than high‐efficiency, energy‐expensive foraging methods. When time is limiting, food is abundant and energy needs are large, as during reproduction, high‐efficiency high‐cost foraging methods give shorter daily foraging times than low‐efficiency low‐cost foraging methods. When time is not limiting, food is abundant, and energy needs are small, the choice of foraging method is not critical. Small animals have lower rates of energy expenditure for locomotion than large animals. At a given food density and with similar diet, small animals are therefore more likely than large ones to minimize foraging time by using high‐efficiency energy‐expansive foraging methods and to exploit patches and sites that require energy‐demanding locomotion modes. Survival selection takes place at food shortages, while low‐efficiency low‐cost foraging methods are used, whereas reproduction selection occurs when food is abundant and high‐efficiency energy‐expensive foraging methods do better. In seasonal environments, selection therefore acts on different foraging methods at different times. Morphological adaptation to one method may oppose adaptation to another. Such conflicts select against foraging and morphological specialization and tend to give species‐poor communities of year‐round resident generalists. But a stable year‐round food supply favors specialization, niche narrowing, and dense species packing.     

Help or hindrance? The evolutionary impact of whole‐genome duplication on immunogenetic diversity and parasite load

Whole‐genome duplication (WGD) events occur in all kingdoms and have been hypothesized to promote adaptability. WGDs identified in the early history of vertebrates, teleosts, and angiosperms have been linked to the large‐scale diversification of these lineages. However, the mechanics and full outcomes of WGD regarding potential evolutionary impacts remain a topic of debate. The Corydoradinae are a diverse subfamily of Neotropical catfishes with over 170 species described and a history of WGDs. They are divided into nine mtDNA lineages, with species coexisting in sympatric—and often mimetic—communities containing representatives of two or more of the nine lineages. Given their similar life histories, coexisting species of Corydoras might be exposed to similar parasite loads and because of their different histories of WGD and genome size they provide a powerful system for investigating the impacts of WGD on immune diversity and function in an animal system. Here, we compared parasite counts and the diversity of the immune‐related toll‐like receptors (TLR) in two coexisting species of Corydoras catfish (C. maculifer and C. araguaiaensis), one diploid and one putative tetraploid. In the putative tetraploid C. araguaiaensis, we found significantly lower numbers of parasites and significantly higher diversity (measured by both synonymous and nonsynonymous SNP counts) in two TLR genes than in the diploid C. maculifer. These results provide insight into how WGD may impact evolution, in this case by providing greater immunogenetic diversity.     

Glucagon signalling in the dorsal vagal complex is sufficient and necessary for high‐protein feeding to regulate glucose homeostasis in vivo

High‐protein feeding acutely lowers postprandial glucose concentration compared to low‐protein feeding, despite a dichotomous rise of circulating glucagon levels. The physiological role of this glucagon rise has been largely overlooked. We here first report that glucagon signalling in the dorsal vagal complex (DVC) of the brain is sufficient to lower glucose production by activating a Gcgr–PKA–ERK–K_ATP channel signalling cascade in the DVC of rats in vivo. We further demonstrate that direct blockade of DVC Gcgr signalling negates the acute ability of high‐ vs. low‐protein feeding to reduce plasma glucose concentration, indicating that the elevated circulating glucagon during high‐protein feeding acts in the brain to lower plasma glucose levels. These data revise the physiological role of glucagon and argue that brain glucagon signalling contributes to glucose homeostasis during dietary protein intake.     

Decay of TRPV3 as the genomic trace of epidermal structure changes in the land‐to‐sea transition of mammals

The epidermis plays an indispensable barrier function in animals. Some species have evolved unique epidermal structures to adapt to different environments. Aquatic and semi‐aquatic mammals (cetaceans, manatees, and hippopotamus) are good models to study the evolution of epidermal structures because of their exceptionally thickened stratum spinosum, the lack of stratum granulosum, and the parakeratotic stratum corneum. This study aimed to analyze an upstream regulatory gene transient receptor potential cation channel, subfamily V, member 3 (TRPV3) of epidermal differentiation so as to explore the association between TRPV3 evolution and epidermal changes in mammals. Inactivating mutations were detected in almost all the aquatic cetaceans and several terrestrial mammals. Relaxed selective pressure was examined in the cetacean lineages with inactivated TRPV3, which might contribute to its exceptionally thickened stratum spinosum as the significant thickening of stratum spinosum in TRPV3 knock‐out mouse. However, functional TRPV3 may exist in several terrestrial mammals due to their strong purifying selection, although they have “inactivating mutations.” Further, for intact sequences, relaxed selective constraints on the TRPV3 gene were also detected in aquatic cetaceans, manatees, and semi‐aquatic hippopotamus. However, they had intact TRPV3, suggesting that the accumulation of inactivating mutations might have lagged behind the relaxed selective pressure. The results of this study revealed the decay of TRPV3 being the genomic trace of epidermal development in aquatic and semi‐aquatic mammals. They provided insights into convergently evolutionary changes of epidermal structures during the transition from the terrestrial to the aquatic environment.     

Context‐dependent outcomes in a reproductive mutualism between two freshwater fish species

1. The development of encompassing general models of ecology is precluded by underrepresentation of certain taxa and systems. Models predicting context‐dependent outcomes of biotic interactions have been tested using plants and bacteria, but their applicability to higher taxa is largely unknown.
2. We examined context dependency in a reproductive mutualism between two stream fish species: mound nest‐building bluehead chub Nocomis leptocephalus and mountain redbelly dace Chrosomus oreas, which often uses N. leptocephalus nests for spawning. We hypothesized that increased predator density and decreased substrate availability would increase the propensity of C. oreas to associate with N. leptocephalus and decrease reproductive success of both species.
3. In a large‐scale in situ experiment, we manipulated egg predator density and presence of both symbionts (biotic context), and replicated the experiment in habitats containing high‐ and low‐quality spawning substrate (abiotic context).
4. Contradictory to our first hypothesis, we observed that C. oreas did not spawn without its host. The interaction outcome switched from commensalistic to mutualistic with changing abiotic and biotic contexts, although the net outcome was mutualistic.
5. The results of this study yielded novel insight into how context dependency operates in vertebrate mutualisms. Although the dilution effect provided by C. oreas positively influenced reproductive success of N. leptocephalus, it was not enough to overcome both egg predation and poor spawning habitat quality. Outcomes of the interaction may be ultimately determined by associate density. Studies of context dependency in vertebrate systems require detailed knowledge of species life‐history traits.

     

Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant

The aphid Schlechtendalia chinensis is an economically important insect that can induce horned galls, which are valuable for the medicinal and chemical industries. Up to now, more than twenty aphid genomes have been reported. Most of the sequenced genomes are derived from free‐living aphids. Here, we generated a high‐quality genome assembly from a galling aphid. The final genome assembly is 271.52 Mb, representing one of the smallest sequenced genomes of aphids. The genome assembly is based on contig and scaffold N50 values of the genome sequence are 3.77 Mb and 20.41 Mb, respectively. Nine‐seven percent of the assembled sequences was anchored onto 13 chromosomes. Based on BUSCO analysis, the assembly involved 96.9% of conserved arthropod and 98.5% of the conserved Hemiptera single‐copy orthologous genes. A total of 14,089 protein‐coding genes were predicted. Phylogenetic analysis revealed that S. chinensis diverged from the common ancestor of Eriosoma lanigerum approximately 57 million years ago (MYA). In addition, 35 genes encoding salivary gland proteins showed differentially when S. chinensis forms a gall, suggesting they have potential roles in gall formation and plant defense suppression. Taken together, this high‐quality S. chinensis genome assembly and annotation provide a solid genetic foundation for future research to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.     

A genotyping‐in‐thousands by sequencing panel to inform invasive deer management using noninvasive fecal and hair samples

Studies in ecology, evolution, and conservation often rely on noninvasive samples, making it challenging to generate large amounts of high‐quality genetic data for many elusive and at‐risk species. We developed and optimized a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel using noninvasive samples to inform the management of invasive Sitka black‐tailed deer (Odocoileus hemionus sitkensis) in Haida Gwaii (Canada). We validated our panel using paired high‐quality tissue and noninvasive fecal and hair samples to simultaneously distinguish individuals, identify sex, and reconstruct kinship among deer sampled across the archipelago, then provided a proof‐of‐concept application using field‐collected feces on SGang Gwaay, an island of high ecological and cultural value. Genotyping success across 244 loci was high (90.3%) and comparable to that of high‐quality tissue samples genotyped using restriction‐site associated DNA sequencing (92.4%), while genotyping discordance between paired high‐quality tissue and noninvasive samples was low (0.50%). The panel will be used to inform future invasive species operations in Haida Gwaii by providing individual and population information to inform management. More broadly, our GT‐seq workflow that includes quality control analyses for targeted SNP selection and a modified protocol may be of wider utility for other studies and systems where noninvasive genetic sampling is employed.     

Characteristics of the mitochondrial genome of Rana omeimontis and related species in Ranidae: Gene rearrangements and phylogenetic relationships

The Omei wood frog (Rana omeimontis), endemic to central China, belongs to the family Ranidae. In this study, we achieved detail knowledge about the mitogenome of the species. The length of the genome is 20,120 bp, including 13 protein‐coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a noncoding control region. Similar to other amphibians, we found that only nine genes (ND6 and eight tRNA genes) are encoded on the light strand (L) and other genes on the heavy strand (H). Totally, The base composition of the mitochondrial genome included 27.29% A, 28.85% T, 28.87% C, and 15.00% G, respectively. The control regions among the Rana species were found to exhibit rich genetic variability and A + T content. R. omeimontis was clustered together with R. chaochiaoensis in phylogenetic tree. Compared to R. amurensis and R. kunyuensi, it was more closely related to R. chaochiaoensis, and a new way of gene rearrangement (ND6‐trnE‐Cytb‐D‐loop‐trnL2 (CUN)‐ND5‐D‐loop) was also found in the mitogenome of R. amurensis and R. kunyuensi. Our results about the mitochondrial genome of R. omeimontis will contribute to the future studies on phylogenetic relationship and the taxonomic status of Rana and related Ranidae species.     

A natural experiment identifies an impending ecological trap for a neotropical amphibian in response to extreme weather events

Extreme weather events are predicted to increase as a result of climate change, yet amphibian responses to extreme disturbance events remain understudied, especially in the Neotropics. Recently, an unprecedented windstorm within a protected Costa Rican rainforest opened large light gaps in sites where we have studied behavioral responses of diurnal strawberry poison frogs (Oophaga pumilio) to ultraviolet radiation for nearly two decades. Previous studies demonstrate that O. pumilio selects and defends perches where ultraviolet radiation (UV‐B) is relatively low, likely because of the lethal and sublethal effects of UV‐B. In this natural experiment, we quantified disturbance to O. pumilio habitat, surveyed for the presence of O. pumilio in both high‐disturbance and low‐disturbance areas of the forest, and assessed UV‐B levels and perch selection behavior in both disturbance levels. Fewer frogs were detected in high‐disturbance habitat than in low‐disturbance habitat. In general, frogs were found vocalizing at perches in both disturbance levels, and in both cases, in significantly lower UV‐B levels relative to ambient adjacent surroundings. However, frogs at perches in high‐disturbance areas were exposed to UV‐B levels nearly 10 times greater than males at perches in low‐disturbance areas. Thus, behavioral avoidance of UV‐B may not reduce the risks associated with elevated exposure under these novel conditions, and similarly, if future climate and human‐driven land‐use change lead to sustained analogous environments.     

Loss of the IR region in conifer plastomes: Changes in the selection pressure and substitution rate of protein‐coding genes

Plastid genomes (plastomes) have a quadripartite structure, but some species have drastically reduced or lost inverted repeat (IR) regions. IR regions are important for genome stability and the evolution rate. In the evolutionary process of gymnosperms, the typical IRs of conifers were lost, possibly affecting the evolutionary rate and selection pressure of genomic protein‐coding genes. In this study, we selected 78 gymnosperm species (51 genera, 13 families) for evolutionary analysis. The selection pressure analysis results showed that negative selection effects were detected in all 50 common genes. Among them, six genes in conifers had higher ω values than non‐conifers, and 12 genes had lower ω values. The evolutionary rate analysis results showed that 9 of 50 common genes differed between conifers and non‐conifers. It is more obvious that in non‐conifers, the rates of psbA (trst, trsv, ratio, dN, dS, and ω) were 2.6‐ to 3.1‐fold of conifers. In conifers, trsv, ratio, dN, dS, and ω of ycf2 were 1.2‐ to 3.6‐fold of non‐conifers. In addition, the evolution rate of ycf2 in the IR was significantly reduced. psbA is undergoing dynamic change, with an abnormally high evolution rate as a small portion of it enters the IR region. Although conifers have lost the typical IR regions, we detected no change in the substitution rate or selection pressure of most protein‐coding genes due to gene function, plant habitat, or newly acquired IRs.     

Spatial and seasonal patterns of fish assemblages in mountain streams of the Ren River,southwest China

The spatial–temporal patterns of fish assemblages in lotic systems can provide useful information in developing effective conservation measures. This study aimed to explore the spatial and seasonal changes in fish assemblages and their association with environmental factors in mountain streams of the Ren River, southwest China. Field investigations were conducted at 18 sites during the rainy and dry seasons in 2017. A total of 1,330 individuals, belonging to three orders, eight families, 19 genera, and 21 species, were collected. Analysis of similarities (ANOSIM) showed that the structure of fish assemblages varied significantly at the spatial scale, but not at the seasonal scale. In low‐order sites, fish assemblages were mainly dominated by cold‐water and rheophilic species (e.g., Rhynchocypris oxycephalus, Scaphesthes macrolepis, Metahomaloptera omeiensis, and Gnathopogon herzensteini), while those in high‐order sites were predominated by warm‐water and eurytopic or stagnophilic species (e.g., Squalidus argentatus, Hemiculter leucisculus, and Zacco platypus). Canonical correspondence analysis (CCA) showed that the fish assemblages were structured by a combination of large‐scale landscape factors (e.g., altitude and C‐link) and small‐scale habitat features (e.g., channel width, water temperature, and depth). Among these factors, landscape had the greatest influence on fish assemblages, while local habitat variables were less important or were only significant in certain seasons.     

Reduced habitat quality increases intrinsic but not ecological costs of reproduction

Although the costs of reproduction are predicted to vary with the quality of the breeding habitat thereby affecting population dynamics and life‐history trade‐offs, empirical evidence for this pattern remains sparse and equivocal. Costs of reproduction can operate through immediate ecological mechanisms or through delayed intrinsic mechanisms. Ignoring these separate pathways might hinder the identification of costs and the understanding of their consequences. We experimentally investigated the survival costs of reproduction for adult little owls (Athene noctua) within a gradient of habitat quality. We supplemented food to nestlings, thereby relieving the parents’ effort for brood provisioning. We used radio‐tracking and Bayesian multistate modeling based on marked recapture and dead recovery to estimate survival rates of adult little owls across the year as a function of food supplementation and habitat characteristics. Food supplementation to nestlings during the breeding season increased parental survival not only during the breeding season but also during the rest of the year. Thus, the low survival of parents of unfed broods likely represents both, strong ecological and strong intrinsic costs of reproduction. However, while immediate ecological costs occurred also in high‐quality habitats, intrinsic costs carrying over to the post‐breeding period occurred only in low‐quality habitats. Our results suggest that immediate costs resulting from ecological mechanisms such as predation, are high also in territories of high habitat quality. Long‐term costs resulting from intrinsic trade‐offs, however, are only paid in low‐quality habitats. Consequently, differential effects of habitat quality on immediate ecological and delayed intrinsic mechanisms can mask the increase of costs of reproduction in low‐quality breeding habitats. Intrinsic costs may represent an underrated mechanism of habitat quality affecting adult survival rate thereby considerably accelerating population decline in degrading habitats. This study therefore highlights the need for a long‐term perspective to fully assess the costs of reproduction and the role of habitat quality in modifying these costs.     

Structural basis for feedforward control in the PINK1/Parkin pathway

PINK1 and parkin constitute a mitochondrial quality control system mutated in Parkinson’s disease. PINK1, a kinase, phosphorylates ubiquitin to recruit parkin, an E3 ubiquitin ligase, to mitochondria. PINK1 controls both parkin localization and activity through phosphorylation of both ubiquitin and the ubiquitin‐like (Ubl) domain of parkin. Here, we observed that phospho‐ubiquitin can bind to two distinct sites on parkin, a high‐affinity site on RING1 that controls parkin localization and a low‐affinity site on RING0 that releases parkin autoinhibition. Surprisingly, ubiquitin vinyl sulfone assays, ITC, and NMR titrations showed that the RING0 site has higher affinity for phospho‐ubiquitin than phosphorylated Ubl in trans. We observed parkin activation by micromolar concentrations of tetra‐phospho‐ubiquitin chains that mimic mitochondria bearing multiple phosphorylated ubiquitins. A chimeric form of parkin with the Ubl domain replaced by ubiquitin was readily activated by PINK1 phosphorylation. In all cases, mutation of the binding site on RING0 abolished parkin activation. The feedforward mechanism of parkin activation confers robustness and rapidity to the PINK1‐parkin pathway and likely represents an intermediate step in its evolutionary development.     

Engineering defensin α‐helix to produce high‐affinity SARS‐CoV‐2 spike protein binding ligands

The binding of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) spike protein to the angiotensin‐converting enzyme 2 (ACE2) receptor expressed on the host cells is a critical initial step for viral infection. This interaction is blocked through competitive inhibition by soluble ACE2 protein. Therefore, developing high‐affinity and cost‐effective ACE2 mimetic ligands that disrupt this protein–protein interaction is a promising strategy for viral diagnostics and therapy. We employed human and plant defensins, a class of small (2–5 kDa) and highly stable proteins containing solvent‐exposed alpha‐helix, conformationally constrained by two disulfide bonds. Therefore, we engineered the amino acid residues on the constrained alpha‐helix of defensins to mimic the critical residues on the ACE2 helix 1 that interact with the SARS‐CoV‐2 spike protein. The engineered proteins (h‐deface2, p‐deface2, and p‐deface2‐MUT) were soluble and purified to homogeneity with a high yield from a bacterial expression system. The proteins demonstrated exceptional thermostability (Tm 70.7°C), high‐affinity binding to the spike protein with apparent K _d values of 54.4 ± 11.3, 33.5 ± 8.2, and 14.4 ± 3.5 nM for h‐deface2, p‐deface2, and p‐deface2‐MUT, respectively, and were used in a diagnostic assay that detected SARS‐CoV‐2 neutralizing antibodies. This work addresses the challenge of developing helical ACE2 mimetics by demonstrating that defensins provide promising scaffolds to engineer alpha‐helices in a constrained form for designing of high‐affinity ligands.     

Sequence comparison of the mitochondrial genomes of five brackish water species of the family Neritidae: Phylogenetic implications and divergence time estimation

Neritids are ancient gastropod species which can live in marine, brackish water, and freshwater environments. In this study, we sequenced and annotated the mitochondrial genomes of five brackish water neritids (i.e., Clithon corona, Clithon lentiginosum, Clithon squarrosum, Neritina iris, and Septaria lineata). The mitogenomes ranged from 15,618 to 15,975 bp, and all contain 13 protein‐coding genes (PCGs), 22 tRNA genes, and two rRNA genes, with a closed ring structure. We calculated the Ka/Ks values of all 13 PCGs of Neritidae species, all ratios are less than 1, under purification selection. Phylogenetic analysis of the 13 PCGs showed that Neritimorpha is a sister group with Vetigastropoda and Caenogastopoda, genus Clithon is a sister group with Neritina and Septaria. Estimation of divergence time for all species of Neritidae showed that the main differentiation of Neritidae occurred in Cenozoic period (65 Mya), C. corona and C. lentiginosum were differentiated in the Cenozoic Neogene, the other three species diverged in the Cenozoic Paleogene. These results will help to better understand the evolutionary position of Neritidae and provide reference for further phylogenetic research on Neritidae species.