Antitropicality and convergent evolution: a case study of Permian neospiriferine brachiopods

Antitropical distribution is a biogeographical pattern characterized by natural occurrences of the same species or members of the same clade in the middle‐ or middle‐to‐high‐latitudinal habitats of both hemispheres, either on land or in marine environments, without appearing in the intervening tropical environments. For most of the noted examples of Permian antitropical distribution, particularly in marine invertebrates, the causes of disjunctions have been mainly linked to either dispersal or vicariance models. Little attention has been paid to other possible mechanisms. This study investigated the antitropicality of some Permian neospiriferine brachiopods through detailed taxonomic revision, comparison of palaeobiogeographical distribution, and a phylogenetic analysis. Several species, previously assigned to Kaninospirifer, are here reassigned to other genera, especially to Fasciculatia in the northern hemisphere and to Quadrospira in the southern hemisphere during the Permian. Both Kaninospirifer and Fasciculatia appear to have been restricted to north‐western Pangea and north‐eastern Asia during the Permian, but there is no robust evidence to suggest their presence in the southern hemisphere to which Imperiospira and Quadrospira were confined. In spite of the distributional separation between the two pairs of neospiriferine genera in the Permian palaeobiogeographical regime, they share considerable numbers of morphological characters, such as a large shell, subdued fasciculation, and reduction of ventral adminicula. Notwithstanding these morphological similarities, our phylogenetic reconstruction of the neospiriferines does not support a close relationship between these genera. This therefore must indicate that these similar morphological features were independently acquired, probably with these taxa living in spatially separate but ecologically compatible environmental conditions in the mid‐latitudinal area of each hemisphere during the Permian. We regard this as an example of convergent evolution.     

Aligned trace fossils from the Utica Shale: implications for mode of life and feeding in the trilobite Triarthrus beckii

The olenid trilobite Triarthrus commonly occurs in nearly monospecific assemblages within otherwise relatively barren black shales. As such, it has been proposed that these trilobites preferred dysoxic or even anoxic habitats and suggested feeding habits range from predation and particle feeding to chemoautotrophism. A unique bedding‐plane assemblage of aligned traces that grade from Rusophycus to Cruziana, with associated Triarthrus beckii carcasses, are described from three localities in the Indian Castle Formation (upper Utica Shale) just below a K‐bentonite bed. Although few body fossils are preserved, it is clear that the 15‐cm‐thick, laterally extensive Thruway K‐bentonite created a unique taphonomic window that preserved the activities of numerous olenid trilobites. Rusophycus and Cruziana, consistently observed in densities above 100 trackways/m², were excavated by the trilobites into the upper surface of a micro‐graded bed, likely a distal turbidite deposit. Sedimentological and trace metal data (Mo, Mn, V and U) support dysoxic but not persistently anoxic conditions through this interval. Measurements from over 500 individual trackways have mean orientations of 259.1° (WSW) at the Myers Rd. locality and 224.59° (SW) at the Dolgeville Dam locality. These orientations are closely similar to independent sedimentological indicators of current transport direction at these sites, which indicates that the trilobites preferentially faced into the prevailing current. The trackways provide compelling evidence that Triarthrus beckii individuals were engaged in feeding, probably assisted by current transport of particles. These results do not support previous suggestions that Triarthrus may have relied upon a chemoautotrophic life habit, but are consistent with suggestions of predation or scavenging from the sediment.     

Carbon footprint of rice production under biochar amendment – a case study in a Chinese rice cropping system

As a controversial strategy to mitigate global warming, biochar application into soil highlights the need for life cycle assessment before large‐scale practice. This study focused on the effect of biochar on carbon footprint of rice production. A field experiment was performed with three treatments: no residue amendment (Control), 6 t ha^?1 yr^?1 corn straw (CS) amendment, and 2.4 t ha^?1 yr^?1 corn straw‐derived biochar amendment (CBC). Carbon footprint was calculated by considering carbon source processes (pyrolysis energy cost, fertilizer and pesticide input, farmwork, and soil greenhouse gas emissions) and carbon sink processes (soil carbon increment and energy offset from pyrolytic gas). On average over three consecutive rice‐growing cycles from year 2011 to 2013, the CS treatment had a much higher carbon intensity of rice (0.68 kg CO₂‐C equivalent (CO₂‐C_e) kg^?1 grain) than that of Control (0.24 kg CO₂‐C_e kg^?1 grain), resulting from large soil CH₄ emissions. Biochar amendment significantly increased soil carbon pool and showed no significant effect on soil total N₂O and CH₄ emissions relative to Control; however, due to a variation in net electric energy input of biochar production based on different pyrolysis settings, carbon intensity of rice under CBC treatment ranged from 0.04 to 0.44 kg CO₂‐C_e kg^?1 grain. The results indicated that biochar strategy had the potential to significantly reduce the carbon footprint of crop production, but the energy‐efficient pyrolysis technique does matter.     

Prospects on the evolutionary mitogenomics of plants: A case study on the olive family (Oleaceae)

The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high‐throughput techniques, we reconstructed complete mitogenomes (ca. 0.7 Mb) and plastomes (ca. 156 kb) for six olive accessions and one Chionanthus. A highly variable organization of mitogenomes was observed at the species level. In olive, two specific chimeric genes were identified in the mitogenome of lineage E3 and may be involved in CMS. Plastid‐derived regions (mtpt) were observed in all reconstructed mitogenomes. Through phylogenetic reconstruction, we demonstrate that multiple integrations of mtpt regions have occurred in Oleaceae, but mtpt regions shared by all members of the olive complex derive from a common ancestor. We then assembled 52 conserved mitochondrial gene regions and complete plastomes of ten additional accessions belonging to tribes Oleeae, Fontanesieae and Forsythieae. Phylogenetic congruence between topologies based on mitochondrial regions and plastomes suggests a strong disequilibrium linkage between both organellar genomes. Finally, while phylogenetic reconstruction based on plastomes fails to resolve the evolutionary history of maternal olive lineages in the Mediterranean area, their phylogenetic relationships were successfully resolved with complete mitogenomes. Overall, our study demonstrates the great potential of using mitochondrial DNA in plant phylogeographic and metagenomic studies.     

Wolverine behavior varies spatially with anthropogenic footprint: implications for conservation and inferences about declines

Understanding a species’ behavioral response to rapid environmental change is an ongoing challenge in modern conservation. Anthropogenic landscape modification, or “human footprint,” is well documented as a central cause of large mammal decline and range contractions where the proximal mechanisms of decline are often contentious. Direct mortality is an obvious cause; alternatively, human‐modified landscapes perceived as unsuitable by some species may contribute to shifts in space use through preferential habitat selection. A useful approach to tease these effects apart is to determine whether behaviors potentially associated with risk vary with human footprint. We hypothesized wolverine (Gulo gulo) behaviors vary with different degrees of human footprint. We quantified metrics of behavior, which we assumed to indicate risk perception, from photographic images from a large existing camera‐trapping dataset collected to understand wolverine distribution in the Rocky Mountains of Alberta, Canada. We systematically deployed 164 camera sites across three study areas covering approximately 24,000 km², sampled monthly between December and April (2007–2013). Wolverine behavior varied markedly across the study areas. Variation in behavior decreased with increasing human footprint. Increasing human footprint may constrain potential variation in behavior, through either restricting behavioral plasticity or individual variation in areas of high human impact. We hypothesize that behavioral constraints may indicate an increase in perceived risk in human‐modified landscapes. Although survival is obviously a key contributor to species population decline and range loss, behavior may also make a significant contribution.     

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea)

The analysis of apex predator diet has the ability to deliver valuable insights into ecosystem health, and the potential impacts a predator might have on commercially relevant species. The Australian sea lion (Neophoca cinerea) is an endemic apex predator and one of the world's most endangered pinnipeds. Given that prey availability is vital to the survival of top predators, this study set out to understand what dietary information DNA metabarcoding could yield from 36 sea lion scats collected across 1,500 km of its distribution in southwest Western Australia. A combination of PCR assays were designed to target a variety of potential sea lion prey, including mammals, fish, crustaceans, cephalopods, and birds. Over 1.2 million metabarcodes identified six classes from three phyla, together representing over 80 taxa. The results confirm that the Australian sea lion is a wide‐ranging opportunistic predator that consumes an array of mainly demersal fauna. Further, the important commercial species Sepioteuthis australis (southern calamari squid) and Panulirus cygnus (western rock lobster) were detected, but were present in <25% of samples. Some of the taxa identified, such as fish, sharks and rays, clarify previous knowledge of sea lion prey, and some, such as eel taxa and two gastropod species, represent new dietary insights. Even with modest sample sizes, a spatial analysis of taxa and operational taxonomic units found within the scat shows significant differences in diet between many of the sample locations and identifies the primary taxa that are driving this variance. This study provides new insights into the diet of this endangered predator and confirms the efficacy of DNA metabarcoding of scat as a noninvasive tool to more broadly define regional biodiversity.     

Dioecy,more than monoecy,affects plant spatial genetic structure: the case study of Ficus

In this analysis, we attempt to understand how monoecy and dioecy drive spatial genetic structure (SGS) in plant populations. For this purpose, plants of the genus Ficus were used as a comparative model due to their particular characteristics, including high species diversity, variation in life histories, and sexual systems. One of the main issues we assessed is whether dioecious fig tree populations are more spatially genetically structured than monoecious populations. Using the Sp statistic, which allows for quantitative comparisons among different studies, we compared the extent of SGS between monoecious and dioecious Ficus species. To broaden our conclusions we used published data on an additional 27 monoecious and dioecious plant species. Furthermore, genetic diversity analyses were performed for two monoecious Ficus species using 12 microsatellite markers in order to strengthen our conclusions about SGS. Our results show that dioecy, more than monoecy, significantly contributes to SGS in plant populations. On average, the estimate of Sp was six times higher for dioecious Ficus species than monoecious Ficus species and it was two times higher in dioecious than monoecious plant species. Considering these results, we emphasize that the long‐distance pollen dispersal mechanism in monoecious Ficus species seems to be the dominant factor in determining weak spatial genetic structure, high levels of genetic diversity, and lack of inbreeding. Although Ficus constitute a model species to study SGS, a more general comparison encompassing a wider range of plants is required in order to better understand how sexual systems affect genetic structure.     

A single‐nucleotide polymorphism of miR‐146a and psoriasis: an association and functional study

Epidermal growth factor receptor (EGFR), which is overexpressed in psoriatic lesions, has been proven to contribute to the hyperproliferation of keratinocytes in psoriasis. Single nucleotide polymorphisms (SNPs) involved in miRNAs that can regulate the expression of EGFR could potentially influence the development of psoriasis. The present study investigated the association between a functional SNP of rs2910164 in miR‐146a and the risk of psoriasis in the Chinese Han population. A total of 521 Han Chinese patients with psoriasis and 582 healthy controls were recruited in this study. The miR‐146a rs2910164 SNP was genotyped by polymerase chain reaction‐restriction fragment length polymorphism. Overall, a significantly increased risk of psoriasis was associated with the rs2910164 miR‐146a CG and GG genotypes (adjusted OR, 1.38; 95% CI, 1.06–1.80). Furthermore, the rs2910164G allele in miR‐146a attenuated its inhibitory regulation on the expression of EGFR as well as the proliferation of human keratinocytes, and lowered the level of miR‐146a in the psoriatic lesions. These findings indicate that the rs2910164G allele in miR‐146a weakens its suppression on the proliferation of keratinocytes probably through the decreased inhibition of the target gene, EGFR, which may account for the increased risk of psoriasis in this study population.     

Hydrodynamic advantages in the free‐living spiriferinide brachiopod Pachycyrtella omanensis: functional insight into adaptation to high‐energy flow environments

Immobile benthic organisms lacking attachment or cementation mechanisms are considered to be best adapted to quiet bottom environments. Since the free‐living Lower Permian spiriferinide brachiopod Pachycyrtella omanensis inhabited a sandy substrate with high‐energy water flow, flume experiments were performed to show the possible hydrodynamic advantages of shell morphology in postural stability and generation of feeding flows. Modelling indicates that a vertical position, with the commissure plane perpendicular to the seabed, was the most unstable, although it is considered to have been its original life position. On the other hand, the passive flow inside the model in vertical position exhibited vortex movement with constant degree of inhalent flow and exhalent flow, conferring advantages on the effective filtration of food particles using a spiral lophophore. The intensity and movement of the passive flow for feeding could have been adjusted through changes in the angle of opening of the valves. As the shoreface habitat was affected by oscillatory flows, a small‐sized animal could have undergone a high risk of burial, while an increase in size would have led to easier removal from the sandy bottom. To avoid both physical risks, Pachycyrtella developed a thick shell with a high rate of growth, specifically increasing the weight of the ventral umbo without altering its morphofunction to generate passive feeding flows. Biomechanics, functional morphology, opportunistic species, Pachycyrtella, Spiriferinida, suspension feeder.     

Bacterial endosymbiont infections in ‘living fossils’: a case study of North American vaejovid scorpions

Bacterial endosymbionts are common among arthropods, and maternally inherited forms can affect the reproductive and behavioural traits of their arthropod hosts. The prevalence of bacterial endosymbionts and their role in scorpion evolution have rarely been investigated. In this study, 61 samples from 40 species of scorpion in the family Vaejovidae were screened for the presence of the bacterial endosymbionts Cardinium, Rickettsia, Spiroplasma and Wolbachia. No samples were infected by these bacteria. However, one primer pair specifically designed to amplify Rickettsia amplified nontarget genes of other taxa. Similar off‐target amplification using another endosymbiont‐specific primer was also found during preliminary screenings. Results caution against the overreliance on previously published screening primers to detect bacterial endosymbionts in host taxa and suggest that primer specificity may be higher in primers targeting nuclear rather than mitochondrial genes.     

Biodiversity of green algae covering artificial hard substrate surfaces in a suburban environment: a case study using molecular approaches

In Middle European suburban environments green algae often cover open surfaces of artificial hard substrates. Microscopy reveals the Apatococcus/Desmococcus morphotype predominant over smaller coccoid forms. Adverse conditions such as limited water availability connected with high PAR and UV irradiance may narrow the algal diversity to a few specialists in these subaerial habitats. We used rRNA gene cloning/sequencing from both DNA extracts of the biofilms without culturing as well as cultures, for the unambiguous determination of the algal composition and to assess the algal diversity more comprehensively. The culture independent approach revealed mainly just two genera (Apatococcus, Trebouxia) for all study sites and five molecular operational taxonomic units (OTUs) for a particular study site, which based on microscopic observation was the one with the highest morphological diversity. The culture approach, however, revealed seven additional OTUs from five genera (Chloroidium, Coccomyxa, Coenochloris, Pabia, Klebsormidium) and an unidentified trebouxiophyte lineage for that same site; only two OTUs were shared by both approaches. Two OTUs or species were recovered for which references have been isolated only from Antarctica so far. However, the internal transcribed spacer (ITS) sequence differences among them supported they are representing distinct populations of the same species. Within Apatococcus five clearly distinct groups of ITS sequences, each putatively representing a distinct species, were recovered with three or four such ITS types co‐occurring at the same study site. Except for the streptophyte Klebsormidium only members of Trebouxiophyceae were detected suggesting these algae may be particularly well‐adapted to subaerial habitats.     

Phylogenomic analysis of gene co‐expression networks reveals the evolution of functional modules

Molecular evolutionary studies correlate genomic and phylogenetic information with the emergence of new traits of organisms. These traits are, however, the consequence of dynamic gene networks composed of functional modules, which might not be captured by genomic analyses. Here, we established a method that combines large‐scale genomic and phylogenetic data with gene co‐expression networks to extensively study the evolutionary make‐up of modules in the moss Physcomitrella patens, and in the angiosperms Arabidopsis thaliana and Oryza sativa (rice). We first show that younger genes are less annotated than older genes. By mapping genomic data onto the co‐expression networks, we found that genes from the same evolutionary period tend to be connected, whereas old and young genes tend to be disconnected. Consequently, the analysis revealed modules that emerged at a specific time in plant evolution. To uncover the evolutionary relationships of the modules that are conserved across the plant kingdom, we added phylogenetic information that revealed duplication and speciation events on the module level. This combined analysis revealed an independent duplication of cell wall modules in bryophytes and angiosperms, suggesting a parallel evolution of cell wall pathways in land plants. We provide an online tool allowing plant researchers to perform these analyses at http://www.gene2function.de .     

Transient expression in Nicotiana benthamiana for rapid functional analysis of genes involved in non‐photochemical quenching and carotenoid biosynthesis

Plants must switch rapidly between light harvesting and photoprotection in response to environmental fluctuations in light intensity. This switch can lead to losses in absorbed energy usage, as photoprotective energy dissipation mechanisms can take minutes to hours to fully relax. One possible way to improve photosynthesis is to engineer these energy dissipation mechanisms (measured as non‐photochemical quenching of chlorophyll a fluorescence, NPQ) to induce and relax more quickly, resulting in smaller losses under dynamic light conditions. Previous studies aimed at understanding the enzymes involved in the regulation of NPQ have relied primarily on labor‐intensive and time‐consuming generation of stable transgenic lines and mutant populations – approaches limited to organisms amenable to genetic manipulation and mapping. To enable rapid functional testing of NPQ‐related genes from diverse organisms, we performed Agrobacterium tumefaciens‐mediated transient expression assays in Nicotiana benthamiana to test if NPQ kinetics could be modified in fully expanded leaves. By expressing Arabidopsis thaliana genes known to be involved in NPQ, we confirmed the viability of this method for studying dynamic photosynthetic processes. Subsequently, we used naturally occurring variation in photosystem II subunit S, a modulator of NPQ in plants, to explore how differences in amino acid sequence affect NPQ capacity and kinetics. Finally, we functionally characterized four predicted carotenoid biosynthesis genes from the marine algae Nannochloropsis oceanica and Thalassiosira pseudonana and examined the effect of their expression on NPQ in N. benthamiana. This method offers a powerful alternative to traditional gene characterization methods by providing a fast and easy platform for assessing gene function in planta.     

Rapid identification of the Asian gypsy moth and its related species based on mitochondrial DNA

The gypsy moth—Lymantria dispar (Linnaeus)—is a worldwide forest defoliator and is of two types: the European gypsy moth and the Asian gypsy moth. Because of multiple invasions of the Asian gypsy moth, the North American Plant Protection Organization officially approved Regional Standards for Phytosanitary Measures No. 33. Accordingly, special quarantine measures have been implemented for 30 special focused ports in the epidemic areas of the Asian gypsy moth, including China, which has imposed great inconvenience on export trade. The Asian gypsy moth and its related species (i.e., Lymantria monocha and Lymantria xylina) intercepted at ports are usually at different life stages, making their identification difficult. Furthermore, Port quarantine requires speedy clearance. As such, it is difficult to identify the Asian gypsy moth and its related species only by their morphological characteristics in a speedy measure. Therefore, this study aimed to use molecular biology technology to rapidly identify the Asian gypsy moth and its related species based on the consistency of mitochondrial DNA in different life stages. We designed 10 pairs of specific primers from different fragments of the Asian gypsy moth and its related species, and their detection sensitivity met the need for rapid identification. In addition, we determined the optimal polymerase chain reaction amplification temperature of the 10 pairs of specific primers, including three pairs of specific primers for the Asian gypsy moth (L. dispar asiatic), four pairs of specific primers for the nun moth (L. monocha), and three pairs of specific primers for the casuarina moth (L. xylina). In conclusion, using our designed primers, direct rapid identification of the Asian gypsy moth and its related species is possible, and this advancement can help improve export trade in China.     

Caterpillars on a phytochemical landscape: The case of alfalfa and the Melissa blue butterfly

Modern metabolomic approaches that generate more comprehensive phytochemical profiles than were previously available are providing new opportunities for understanding plant‐animal interactions. Specifically, we can characterize the phytochemical landscape by asking how a larger number of individual compounds affect herbivores and how compounds covary among plants. Here we use the recent colonization of alfalfa (Medicago sativa) by the Melissa blue butterfly (Lycaeides melissa) to investigate the effects of indivdiual compounds and suites of covarying phytochemicals on caterpillar performance. We find that survival, development time, and adult weight are all associated with variation in nutrition and toxicity, including biomolecules associated with plant cell function as well as putative anti‐herbivore action. The plant‐insect interface is complex, with clusters of covarying compounds in many cases encompassing divergent effects on different aspects of caterpillar performance. Individual compounds with the strongest associations are largely specialized metabolites, including alkaloids, phenolic glycosides, and saponins. The saponins are represented in our data by more than 25 individual compounds with beneficial and detrimental effects on L. melissa caterpillars, which highlights the value of metabolomic data as opposed to approaches that rely on total concentrations within broad defensive classes.