Adult hippocampal neurogenesis of mammals: evolution and life history

Substantial production of new neurons in the adult mammalian brain is restricted to the olfactory system and the hippocampal formation. Its physiological and behavioural role is still debated. By comparing adult hippocampal neurogenesis (AHN) across many mammalian species, one might recognize a common function. AHN is most prominent in rodents, but shows considerable variability across species, being lowest or missing in primates and bats. The latter finding argues against a critical role of AHN in spatial learning and memory. The common functional denominator across all species investigated thus far is a strong decline of AHN from infancy to midlife. As predicted by Altman and colleagues in 1973, this implies a role in transforming juvenile unpredictable to predictable behaviour, typically characterizing mammalian behaviour once reproductive competence has been attained. However, as only a fraction of mammalian species has been investigated, further comparative studies are necessary in order to recognize whether AHN has a common unique function, or whether it mediates species-specific hippocampal functions.     

Experimental design and taxonomic scope of fragmentation studies on European mammals: current status and future priorities

• 1 Habitat loss, habitat fragmentation and habitat degradation are the greatest threats to mammals in Europe and the rest of the world. Despite the fact that extensive literature exists, no comprehensive review or synthesis is available to date and this may slow down scientific progress and hamper conservation efforts.
• 2 The goal of this study is to understand if and in what direction progress has been made in the study of the effects of habitat loss and fragmentation on the spatial distribution of European terrestrial mammals. Firstly, we carry out a general synthesis which is structured around 11 key points. The aim of this point‐by‐point analysis is to identify trends, knowledge gaps and any significant bias in the available literature, and to highlight strengths and shortfalls of the different approaches which have to date been applied. Secondly, we follow a species‐specific systematic approach: for each species, we synthesise key results.
• 3 Our results show how substantial progress has been hampered for several reasons including: a large predominance of small‐scale field studies of short duration, and a generalised lack of control of: (i) confounding variables; (ii) spatial autocorrelation; and (iii) false absences. Also, despite the relatively high number of studies, few were theoretical studies and even fewer were meta‐analyses. The lack of meta‐analyses is likely to be due to the small amount of crucial details included in the publications, such as model parameters or information on the landscape context (such as the amount of residual forest cover).
• 4 We synthesise the main results for 14 species. The level of progress is highly variable: for some species, such as the red squirrel Sciurus vulgaris, a series of long‐term, large‐scale process‐oriented studies has allowed an in‐depth understanding of its ecology in fragmented landscapes. On the other hand, with other species such as the bank vole Myodes glareolus, despite a relatively large number of field studies, little progress has been made.

     

Diversity patterns in a diversity hotspot

Our knowledge of diversity patterns is generally founded on studies performed in the more species‐poor part of our globe. Ibanez et al. (2014, this issue) report on patterns based on impressive field efforts in a diversity hotspot, namely New Caledonia. Some intriguing patterns arise from this study offering valuable insights in our quest to understand and manage global biodiversity.     

α2‐glycine receptors modulate adult hippocampal neurogenesis and spatial memory

The α2‐glycine receptors (GlyRs) play important roles during early central nervous system development. However, these receptors’ possible involvement in neurodevelopmental events occurring in the adult brain remains to be explored. Adult hippocampal neurogenesis (AHN) is the process by which new granule cell neurons are added to the dentate gyrus (DG) throughout adulthood. In this study, we observed that hippocampal adult neural stem cells (ANSCs) express α2‐containing GlyRs. Pharmacological inhibition of GlyRs by strychnine or picrotoxin decreased the proliferation of ANSCs, both in vivo and in vitro . Mice knockout for glra2 , the gene coding for the GlyR α2 subunit, were determined to display impaired AHN, and this phenomenon was accompanied by deficits in spatial memory. These results, which reveal neurodevelopmental roles for α2‐GlyRs in the adult brain, may be clinically relevant, given that a mutation in GLAR2 , as well as AHN impairments, have been reported in autism spectrum disorder. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 77: 1430–1441, 2017     

Towards a cohesive,holistic view of top predation: a definition,synthesis and perspective

Research on the ecology of top predators – upper trophic level consumers that are relatively free from predation once they reach adult size – has provided regular contributions to general ecology and is a rapidly expanding and increasingly experimental, multidisciplinary and technological endeavour. Yet, an exponentially expanding literature coupled with rapid disintegration into specialized, disconnected subfields for study (e.g. vertebrate predators versus invertebrate predators, community ecology versus biological control etc.) increasingly means that we are losing a coherent, integrated understating of the role and importance of these species in ecosystems. This process of canalization is likely to hinder sharing of scientific discovery and continued progress, especially as there is a growing need to understand the generality of the top–down forcing, as demonstrated for some members of this group. Here, we propose ways to facilitate synthesis by promoting changes in mentality and awareness among specialists through increased debate and collaboration, conceptual reviews and a series of exemplary case studies. The strategy will rely on the collective contribution by all scientists in the field and will strive to consolidate and formalise top‐order predation as a holistic, cohesive, cross‐taxonomical field of research studying the ecology, evolution and behaviour of apex predators and their capability to exert top–down forcing on lower trophic levels. Synthesis The ongoing global loss of top predators and their recolonization of various regions are causing a rapid upsurge of studies on these species and a consequent fragmentation of this field into disconnected, specialized subcompartments: this will weaken efforts to produce synthetic generalisations of broader ecological interest. Here, we show that top predation provides regular contributions to general ecology, is well grounded in theoretical ecology and is a rapidly expanding and increasingly experimental, multidisciplinary and technological field of research. The novelty of this forum lies in providing a concise synthesis of this area of ecology, in attempting to formalise “top predation” as a specific, inter‐connected area of investigation, and in proposing a marked change of mentality by stressing the need for cross‐taxonomic approaches enabling broader views of the role of predators in ecosystems.     

Promise and progress in environmental genomics: a status report on the applications of gene expression-based microarray studies in ecologically relevant fish species

The advent of any new technology is typically met with great excitement. So it was a few years ago, when the combination of advances in sequencing technology and the development of microarray technology made measurements of global gene expression in ecologically relevant species possible. Many of the review papers published around that time promised that these new technologies would revolutionize environmental biology as they had revolutionized medicine and related fields. A few years have passed since these technological advancements have been made, and the use of microarray studies in non‐model fish species has been adopted in many laboratories internationally. Has the relatively widespread adoption of this technology really revolutionized the fields of environmental biology, including ecotoxicology, aquaculture and ecology, as promised? Or have these studies merely become a novelty and a potential distraction for scientists addressing environmentally relevant questions? In this review, the promises made in early review papers, in particular about the advances that the use of microarrays would enable, are summarized; these claims are compared to the results of recent studies to determine whether the forecasted changes have materialized. Some applications, as discussed in the paper, have been realized and have led to advances in their field, others are still under development.     

A synthesis of laboratory and field studies on the effects of transgenic Bacillus thuringiensis (Bt) maize on non‐target Lepidoptera

One of the major applications of transgenic crops in agriculture are the so‐called Bacillus thuringiensis Berliner (Bt) plants, in particular Bt maizes, which produce insecticidal Cry proteins that target specific orders, such as the Lepidoptera or Coleoptera. We reviewed publications that reported on the direct toxic effects of Bt‐maize and/or Cry proteins of current Bt‐maize events on larvae of non‐target butterflies and moths (Lepidoptera). In total, 20 peer‐reviewed publications were identified, of which 16 papers contributed laboratory‐based data and seven field‐based data. An adverse effect on caterpillars was recorded in 52% of all laboratory‐based and in 21% of all field‐based observations. The variables most often studied and having the highest occurrence of effects were larval survival, body mass, and developmental time. Parameters of the adult stage were under‐represented in the studies. Overall, 11 lepidopteran species were tested. The majority of the studies originated from the USA, with the Monarch butterfly being the most studied, whereas other species and other parts of the world were widely neglected. Laboratory experiments were often run under unrealistic conditions from an ecological point of view. Although the papers we reviewed indicated a potential hazard for Lepidoptera that are exposed to and feed on lepidopteran‐specific Bt‐maize pollen, a general conclusion on the level of risk for butterflies and moths cannot as yet be drawn. A comprehensive risk characterization would require thorough hazard identification, exposure assessment, and impact assessment. However, our review showed that even the basic level of hazard characterization is as yet incomplete. Reasons for this are the still‐limited numbers of publications and concurrent lack of knowledge, the restriction of data to only a few species, the over‐representation of North American species, and the identified limitations of both laboratory and field experiments. The findings of this review suggest that more realistic, ecologically meaningful, and detailed experiments and analyses are crucial to improve the present assessment of Bt‐maize cultivation effects on Lepidoptera.     

Assessment of esterase gene expression as a risk marker for insecticide resistance in Florida Culex nigripalpus (Diptera: Culicidae)

Esterases are enzymatic proteins known to play a role in insecticide resistance formation. To further our understanding of the development of insecticide resistance, we tested the gene expression level of a gene implicated in insecticide resistance (Temsha est‐1) from Culex nigripalpus Theobald (Diptera: Culicidae) in field mosquitoes. We found that the level of expression of TE‐1 differed depending on the frequency of exposure to organophosphate insecticide through expression studies. Temsha est‐1 cDNA is 1,808 base pairs and fully sequenced with up to 96% nucleotide sequence identity to esterase B genes of other mosquito species. The genes from five different species, including TE‐1, were closely related by genetic distance and phylogenetic analysis. Differential expression of this gene that is correlated to differences in susceptibility towards organophosphate would provide the ability to use Temsha est‐1 as an indicator of the formation of tolerance/resistance. This would greatly enhance mosquito control efforts by allowing targeted application of insecticides to mosquito populations that are most susceptible. Also, it would provide resistance information so that a rational design could be used for insecticide rotation schedules.     

Codon usage bias: causative factors,quantification methods and genome‐wide patterns: with emphasis on insect genomes

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole‐genome sequencing of numerous species, both prokaryotes and eukaryotes, genome‐wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole‐genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome‐sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome‐sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.     

Trichomes of Lycopersicon species and their hybrids: effects on pests and natural enemies

1 The cultivated tomato, Lycopersicon esculentum, is an economically important worldwide crop. Current pest management techniques rely heavily on pesticides but trichome‐based host‐plant resistance may reduce pesticide use. 2 A review of the literature is provided on trichomes of wild Lycopersicon species and the effects of trichome‐based host‐plant resistance on arthropods. Solvents have been used to remove glandular trichome exudates and the resulting dimminution of their effects quantified. Correlational approaches to assess the relationship between the different trichome types and effects on pests have also been used. 3 Most studies have focused on Lepidoptera and Hemiptera, although some work has included Coleoptera, Diptera and Acarina, and both antibiotic and antixenotic effects have been demonstrated. 4 Natural enemies are a cornerstone of international pest management and this review discusses how the compatibility of this approach with trichome‐based host‐plant resistance is uncertain because of the reported negative effects of trichomes on one dipteran, one hemipteran and several Hymenoptera. 5 For trichome‐based host‐plant resistance to be utilized as a pest management tool, trichomes of wild species need to be introgressed into the cultivated tomato. Hybrids between the cultivated tomato and the wild species Lycopersicon hirsutum f. glabratum, Lycopersicon pennellii and Lycopersicon cheesmanii f. minor have been produced and useful levels of resistance to Acarina, Diptera and Hemiptera pests have been exhibited, although these effects may be tempered by effects on natural enemies. 6 This review proposes that studies on genetic links between fruit quality and resistance, field studies to determine the compatibility of natural enemies and trichome‐based host‐plant resistance, and a strong focus on L. cheesmanii f. minor, are all priorities for further research that will help realize the potential of this natural defence mechanism in pest management.     

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli

The genome‐scale model (GEM) of metabolism in the bacterium Escherichia coli K‐12 has been in development for over a decade and is now in wide use. GEM‐enabled studies of E. coli have been primarily focused on six applications: (1) metabolic engineering, (2) model‐driven discovery, (3) prediction of cellular phenotypes, (4) analysis of biological network properties, (5) studies of evolutionary processes, and (6) models of interspecies interactions. In this review, we provide an overview of these applications along with a critical assessment of their successes and limitations, and a perspective on likely future developments in the field. Taken together, the studies performed over the past decade have established a genome‐scale mechanistic understanding of genotype–phenotype relationships in E. coli metabolism that forms the basis for similar efforts for other microbial species. Future challenges include the expansion of GEMs by integrating additional cellular processes beyond metabolism, the identification of key constraints based on emerging data types, and the development of computational methods able to handle such large‐scale network models with sufficient accuracy.     

Trichomes of Lycopersicon species and their hybrids: effects on pests and natural enemies

1 The cultivated tomato, Lycopersicon esculentum, is an economically important worldwide crop. Current pest management techniques rely heavily on pesticides but trichome‐based host‐plant resistance may reduce pesticide use. 2 A review of the literature is provided on trichomes of wild Lycopersicon species and the effects of trichome‐based host‐plant resistance on arthropods. Solvents have been used to remove glandular trichome exudates and the resulting dimminution of their effects quantified. Correlational approaches to assess the relationship between the different trichome types and effects on pests have also been used. 3 Most studies have focused on Lepidoptera and Hemiptera, although some work has included Coleoptera, Diptera and Acarina, and both antibiotic and antixenotic effects have been demonstrated. 4 Natural enemies are a cornerstone of international pest management and this review discusses how the compatibility of this approach with trichome‐based host‐plant resistance is uncertain because of the reported negative effects of trichomes on one dipteran, one hemipteran and several Hymenoptera. 5 For trichome‐based host‐plant resistance to be utilized as a pest management tool, trichomes of wild species need to be introgressed into the cultivated tomato. Hybrids between the cultivated tomato and the wild species Lycopersicon hirsutum f. glabratum, Lycopersicon pennellii and Lycopersicon cheesmanii f. minor have been produced and useful levels of resistance to Acarina, Diptera and Hemiptera pests have been exhibited, although these effects may be tempered by effects on natural enemies. 6 This review proposes that studies on genetic links between fruit quality and resistance, field studies to determine the compatibility of natural enemies and trichome‐based host‐plant resistance, and a strong focus on L. cheesmanii f. minor, are all priorities for further research that will help realize the potential of this natural defence mechanism in pest management.     

Sexual selection in a tropical fruit fly: role of a plant derived chemical in mate choice

The specific mechanisms by which selective pressures affect individuals are often difficult to resolve. In tephritid fruit flies, males respond strongly and positively to certain plant derived chemicals. Sexual selection by female choice has been hypothesized as the mechanism driving this behaviour in certain species, as females preferentially mate with males that have fed on these chemicals. This hypothesis is, to date, based on studies of only very few species and its generality is largely untested. We tested the hypothesis on different spatial scales (small cage and seminatural field‐cage) using the monophagous fruit fly, Bactrocera cacuminata. This species is known to respond to methyl eugenol (ME), a chemical found in many plant species and one upon which previous studies have focused. Contrary to expectation, no obvious female choice was apparent in selecting ME‐fed males over unfed males as measured by the number of matings achieved over time, copulation duration, or time of copulation initiation. However, the number of matings achieved by ME‐fed males was significantly greater than unfed males 16 and 32 days after exposure to ME in small cages (but not in a field‐cage). This delayed advantage suggests that ME may not influence the pheromone system of B. cacuminata but may have other consequences, acting on some other fitness consequence (e.g., enhancement of physiology or survival) of male exposure to these chemicals. We discuss the ecological and evolutionary implications of our findings to explore alternate hypotheses to explain the patterns of response of dacine fruit flies to specific plant‐derived chemicals.     

Rating the rat: global patterns and research priorities in impacts and management of rodent pests

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Habitat use, diet and roost selection by the Big Brown Bat (Eptesicus fuscus) in North America: a case for conserving an abundant species

Insectivorous bats are integral components of terrestrial ecosystems. Despite this, a growing number of factors causing world‐wide declines in bat populations have been identified. Relatively abundant species are important for bat conservation because of their role in ecosystems and the research opportunities they offer. In addition, species that have been well‐studied present unique opportunities to synthesize information and highlight important areas of focus for conservation and research. This paper focuses on a well‐studied abundant bat, Eptesicus fuscus. I review the relevant literature on habitat use, diet and roost selection by E. fuscus in North America, and highlight important areas of conservation and research for this species, including the effects of roost disturbance, control of economically important insect pests, exposure to pesticides, long‐term monitoring of populations, and the potential consequences of expanding populations. These issues have broad implications for other species and can be used to focus future research and conservation efforts.     

Conservation genomics in the fight to help the recovery of the critically endangered Siamese crocodile Crocodylus siamensis

Endangered species are often characterized by low genetic diversity and it is imperative for conservation efforts to incorporate the knowledge obtained from genetic studies for effective management. However, despite the promise of technological advances in sequencing, application of genome‐wide data to endangered populations remains uncommon. In the present study we pursued a holistic conservation‐genomic approach to inform a field‐based management programme of a Critically Endangered species, the Siamese crocodile Crocodylus siamensis. Using thousands of single nucleotide polymorphisms from throughout the genome, we revealed signals of introgression from two other crocodile species within our sample of both wild and captive‐bred Siamese crocodiles from Cambodia. Our genetic screening of the Siamese crocodiles resulted in the subsequent re‐introduction of 12 individuals into the wild as well as the selection of four individuals for captive breeding programmes. Comparison of intraspecific genetic diversity revealed an alarmingly low contemporary effective population size in the wild (<50) with evidence of a recent bottleneck around Tonle Sap Lake. We also projected a probable future extinction in the wild (within fewer than five generations) in this population in the absence of re‐introduction efforts. However, an increase in the number of potential breeders through re‐introductions, including the one resulting from this project, could counter this trend. Our results have been implemented in ongoing re‐introduction and captive breeding programmes, with major implications for the conservation management of Siamese crocodiles, and provide a blueprint for the rescue effort of other “terminally ill” populations of critically endangered species.     

Crop genome‐wide association study: a harvest of biological relevance

With the advent of rapid genotyping and next‐generation sequencing technologies, genome‐wide association study (GWAS) has become a routine strategy for decoding genotype–phenotype associations in many species. More than 1000 such studies over the last decade have revealed substantial genotype–phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyond the many ‘hits’ obtained, this review summarizes recent efforts to increase our understanding of the genetic architecture of complex traits by focusing on non‐main effects including epistasis, pleiotropy, and phenotypic plasticity. We also discuss how these achievements and the remaining gaps in our knowledge will guide future studies. Synthetic association is highlighted as leading to false causality, which is prevalent but largely underestimated. Furthermore, validation evidence is appealing for future GWAS, especially in the context of emerging genome‐editing technologies.     

Insular bats and research effort: a review of global patterns and priorities

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Associational effects and the maintenance of polymorphism in plant defense against herbivores: review and evidence

Many plant species have evolved defense traits against herbivores. Associational effects (AEs) refer to a kind of apparent interaction where the herbivory risk to a focal plant species depends on the composition of other plant species in a neighborhood. Despite ample evidence for AEs between different plant species, this point of view has rarely been applied to polymorphism in defense traits within a plant species. The purpose of this review is to highlight an overlooked role of conspecific AEs in maintaining polymorphism in antiherbivore defense. First, I present a general review of AE between plant species and its role in the coexistence of plant species. This viewpoint of AE can be applied to genetic polymorphism within a plant species, as it causes frequency‐ and density‐dependent herbivory between multiple plant types. Second, I introduce a case study of conspecific AEs in the trichome‐producing (hairy) and glabrous plants of Arabidopsis halleri subsp. gemmifera. Laboratory and semi‐field experiments illustrated that AEs against the brassica leaf beetle Phaedon brassicae mediate a minority advantage in defense and fitness between hairy and glabrous plants. Combined with a statistical modeling approach, field observation revealed that conspecific AEs can maintain the trichome dimorphism via negative frequency‐dependent selection in a plant population. Finally, I discuss spatial and temporal scales at which AEs contribute to shaping genetic variation in antiherbivore defense in a plant metapopulation. Based on the review and evidence, I suggest that AEs play a key role in the maintenance of genetic variation within a plant species.     

The biodiversity–ecosystem service relationship in urban areas: a quantitative review

By 2050, up to 75% of people globally will live in cities. Despite the potential ramifications of this urbanization for ecosystem services (ES), and the importance of locally produced ES for the health and wellbeing of urban residents, syntheses addressing the underlying ecology of ES provision rarely include urban areas. Here, I conduct a quantitative review of urban ES studies in the ecological literature, synthesizing trends across the discipline. I also quantify the extent to which this work considers the organisms and ecosystem components responsible for ES provision using two approaches: assessment of biodiversity–ES relationships, and an adaptation of the service provider concept. The majority of urban ES studies were conducted in western, developed countries, and typically assessed a single service in a single city – largely ignoring ES synergies and tradeoffs, and cross‐city comparisons. While several different ES are studied in urban ecosystems, the field is dominated by weather and climate‐related regulating services, with assessments of cultural services particularly lacking. Most studies described a habitat type as the service provider; however, studies that considered the biodiversity–ES relationship were more likely to identify a specific functional group, community, or population as the key provider of an ES. The biodiversity–ES relationship itself was most frequently characterized as dependent on the composition of species, functional traits, or structures, rather than correlated with the magnitude of any specific biodiversity metric. While the study of ES in urban ecosystems is increasing, there exists considerable room for further research. Future studies would benefit by expanding the number and categories of ES assessed within and across cities, as well as broadening the geographical scope of urban ES research. Biodiversity–ES assessments in urban ecosystems would also benefit from an expansion of the biodiversity types considered, particularly regarding non‐species based approaches, and consideration of non‐native and invasive species. Synthesis Urban ecosystem services (ES) affect the health and wellbeing of over 3.5 billion people who live in cities. However, syntheses addressing ES provision rarely include urban areas. I conducted the first quantitative review focused explicitly on the ecology of urban ES, including the role of biodiversity in service provision. I found that studies typically measure only a single service in one city, precluding assessment of ES synergies, tradeoffs, and cross‐city comparisons. I also found that while most studies attribute ES provision to a habitat or land‐use type, studies that consider biodiversity‐ES relationships are more likely to recognize a specific functional group, community, or population as the key provider of an ES.