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In the absence of long-term monitoring data, inferences about extinctions of species and populations are generally based on past observations about the presence of a particular species at specified places and times (sightings). Several methods have been developed to estimate the probability and timing of extinctions from records of such sightings, but they differ in their computational complexity and assumptions about the nature of the sighting record. Here we use simulations to evaluate the performance of seven methods proposed to estimate the upper confidence limit on extinction times under different extinction and sampling scenarios. Our results show that the ability of existing methods to correctly estimate the timing of extinctions varies with the type of extinction (sudden vs. gradual) and the nature of sampling effort over time. When the probability of sampling a species declines over time, many of the methods perform poorly. On the other hand, the simulation results also suggest that as long as the choice of the method is determined by the nature of the underlying sighting data, existing methods should provide reliable inferences about the timing of past extinctions. [ABSTRACT FROM AUTHOR]

Copyright of Applications in Plant Sciences is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Since its immigration in the Pacific island of New Caledonia in 1942 (i.e. about 240 tick-generations ago), the cattle tick Boophilus microplus has experienced a remarkable adaptive diversification there. In order to better understand the population factors involved, we have investigated the B. microplus population structure on that main host-species, Bos taurus. This study was based microsatellite loci and confirmed that the island colonization came along with a significant bottleneck. Knowledge on B. microplus biology led us to expect B. microplus populations to be composed of highly inbred lineages irregularly dispatched among the individual hosts belonging to the same herds. Instead, this study evidenced a weak inbreeding level and an absence of genetic differentiation within herds. Complementarily, a significant signal of isolation by distance exhibited that human-traffic of cattle does not promote high tick dispersal within the island. Finally, the tick density was found to be about a few hundreds of reproducing adults per squared kilometre, for a gene dispersal range of about a few hundred metres per tick generation. Results are discussed with regard to the evolution of new adaptive changes. [ABSTRACT FROM AUTHOR]

Annual grain crops dominate agricultural landscapes and provide the majority of calories consumed by humanity. Perennial grain crops could potentially ameliorate the land degradation and off-site impacts associated with annual grain cropping. However, herbaceous perennial plants with constitutively high allocation to harvestable seeds are rare to absent in nature. Recent trade-off theory models suggest that rugged fitness landscapes may explain the absence of this form better than sink competition models. Artificial selection for both grain production and multiyear lifespan can lead to more rapid progress in the face of fitness and genetic trade-offs than natural selection but is likely to result in plant types that differ substantially from all current domestic crops. Perennial grain domestication is also likely to require the development of selection strategies that differ from published crop breeding methods, despite their success in improving long-domesticated crops; for this purpose, we have reviewed literature in the areas of population and evolutionary genetics, domestication, and molecular biology. Rapid domestication will likely require genes with large effect that are expected to exhibit strong pleiotropy and epistasis. Cryptic genetic variation will need to be deliberately exposed both to purge mildly deleterious alleles and to generate novel agronomic phenotypes. We predict that perennial grain domestication programs will benefit from population subdivision followed by selection for simple traits in each subpopulation, the evaluation of very large populations, high selection intensity, rapid cycling through generations, and heterosis. The latter may be particularly beneficial in the development of varieties with stable yield and tolerance to crowding. [ABSTRACT FROM AUTHOR]

Global change biology has been entering a big data era due to the vast increase in availability of both environmental and biological data. Big data refers to large data volume, complex data sets, and multiple data sources. The recent use of such big data is improving our understanding of interactions between biological systems and global environmental changes. In this review, we first explore how big data has been analyzed to identify the general patterns of biological responses to global changes at scales from gene to ecosystem. After that, we investigate how observational networks and space‐based big data have facilitated the discovery of emergent mechanisms and phenomena on the regional and global scales. Then, we evaluate the predictions of terrestrial biosphere under global changes by big modeling data. Finally, we introduce some methods to extract knowledge from big data, such as meta‐analysis, machine learning, traceability analysis, and data assimilation. The big data has opened new research opportunities, especially for developing new data‐driven theories for improving biological predictions in Earth system models, tracing global change impacts across different organismic levels, and constructing cyberinfrastructure tools to accelerate the pace of model‐data integrations. These efforts will uncork the bottleneck of using big data to understand biological responses and adaptations to future global changes. [ABSTRACT FROM AUTHOR]

The hallmarks of aging have been influential in guiding the biology of aging research, with more recent and growing recognition of the interdependence of these hallmarks on age‐related health outcomes. However, a current challenge is personalizing aging trajectories to promote healthy aging, given the diversity of genotypes and lived experience. We suggest that incorporating heterogeneity—including intrinsic (e.g., genetic and structural) and extrinsic (e.g., environmental and exposome) factors and their interdependence of hallmarks—may move the dial. This editorial perspective will focus on one hallmark, namely mitochondrial dysfunction, to exemplify how consideration of heterogeneity and interdependence or crosstalk may reveal new perspectives and opportunities for personalizing aging research. To this end, we highlight heterogeneity within mitochondria as a model. [ABSTRACT FROM AUTHOR]

Landscape genetic approaches offer the promise of increasing our understanding of the influence of habitat features on genetic structure. We assessed the genetic diversity of the endangered golden-cheeked warbler ( Dendroica chrysoparia) across their breeding range in central Texas and evaluated the role of habitat loss and fragmentation in shaping the population structure of the species. We determined genotypes across nine microsatellite loci of 109 individuals from seven sites representing the major breeding concentrations of the species. No evidence of a recent population bottleneck was found. Differences in allele frequencies were highly significant among sites. The sampled sites do not appear to represent isolated lineages requiring protection as separate management units, although the amount of current gene flow is insufficient to prevent genetic differentiation. Measures of genetic differentiation were negatively associated with habitat connectivity and the percentage of forest cover between sites, and positively associated with geographic distance and the percentage of agricultural land between sites. The northernmost site was the most genetically differentiated and was isolated from other sites by agricultural lands. Fragmentation of breeding habitat may represent barriers to dispersal of birds which would pose no barrier to movement during other activities such as migration. [ABSTRACT FROM AUTHOR]

Shape is data and data is shape. Biologists are accustomed to thinking about how the shape of biomolecules, cells, tissues, and organisms arise from the effects of genetics, development, and the environment. Less often do we consider that data itself has shape and structure, or that it is possible to measure the shape of data and analyze it. Here, we review applications of topological data analysis (TDA) to biology in a way accessible to biologists and applied mathematicians alike. TDA uses principles from algebraic topology to comprehensively measure shape in data sets. Using a function that relates the similarity of data points to each other, we can monitor the evolution of topological features—connected components, loops, and voids. This evolution, a topological signature, concisely summarizes large, complex data sets. We first provide a TDA primer for biologists before exploring the use of TDA across biological sub‐disciplines, spanning structural biology, molecular biology, evolution, and development. We end by comparing and contrasting different TDA approaches and the potential for their use in biology. The vision of TDA, that data are shape and shape is data, will be relevant as biology transitions into a data‐driven era where the meaningful interpretation of large data sets is a limiting factor. [ABSTRACT FROM AUTHOR]

Bioelectricity is the electrical activity that occurs within living cells and tissues. This activity is critical for regulating homeostatic cellular function and communication, and disruptions of the same can lead to a variety of conditions, including cancer. Cancer cells are known to exhibit abnormal electrical properties compared to their healthy counterparts, and this has driven researchers to investigate the potential of harnessing bioelectricity as a tool in cancer diagnosis, prognosis, and treatment. In parallel, bioelectricity represents one of the means to gain fundamental insights on how electrical signals and charges play a role in cancer insurgence, growth, and progression. This review provides a comprehensive analysis of the literature in this field, addressing the fundamentals of bioelectricity in single cancer cells, cancer cell cohorts, and cancerous tissues. The emerging role of bioelectricity in cancer proliferation and metastasis is introduced. Based on the acknowledgement that this biological information is still hard to access due to the existing gap between biological findings and translational medicine, the latest advancements in the field of nanotechnologies for cellular electrophysiology are examined, as well as the most recent developments in micro‐ and nano‐devices for cancer diagnostics and therapy targeting bioelectricity. [ABSTRACT FROM AUTHOR]

Here, high-throughput tomography (HiTT), a fast and versatile phase-contrast imaging platform for life-science samples on the EMBL beamline P14 at DESY in Hamburg, Germany, is presented. A high-photon-flux undulator beamline is used to perform tomographic phase-contrast acquisition in about two minutes which is linked to an automated data processing pipeline that delivers a 3D reconstructed data set less than a minute and a half after the completion of the X-ray scan. Combining this workflow with a sophisticated robotic sample changer enables the streamlined collection and reconstruction of X-ray imaging data from potentially hundreds of samples during a beam-time shift. HiTT permits optimal data collection for many different samples and makes possible the imaging of large sample cohorts thus allowing population studies to be attempted. The successful application of HiTT on various soft tissue samples in both liquid (hydrated and also dehydrated) and paraffin-embedded preparations is demonstrated. Furthermore, the feasibility of HiTT to be used as a targeting tool for volume electron microscopy, as well as using HiTT to study plant morphology, is demonstrated. It is also shown how the high-throughput nature of the work has allowed large numbers of 'identical' samples to be imaged to enable statistically relevant sample volumes to be studied. [ABSTRACT FROM AUTHOR]

Many alpine species are under threat from global climate change, as their geographic ranges become increasingly fragmented and unsuitable. Understanding rates and determinants of gene flow among such fragmented populations, over historical as well as recent timescales, can help to identify populations under threat. It is also important to clarify the degree to which loss of local populations reduces overall genetic diversity within the taxon. The endangered Blue Mountains Water Skink ( Eulamprus leuraensis) is restricted to <40 small swamps in montane south-eastern Australia. Our analyses of seven microsatellite loci of 241 animals from 13 populations show strong geographic structure, with major genetic divergence even between populations separated by <0.5 km. Dispersal between populations is scarce, and appears to involve mostly males. Our analyses suggest potential recent bottleneck events in all the identified populations, and lower genetic diversity and population size parameter at lower-elevation sites than at higher-elevation sites. Management of this endangered taxon thus needs to treat most populations separately, because of their genetic distinctiveness and low rates of genetic exchange. [ABSTRACT FROM AUTHOR]

1. Genetic variation at five microsatellite loci was investigated in six sea trout ( Salmo trutta) populations to describe their spatio-temporal genetic variation in north-western Spain. We observed significant genetic variation between river basins, and isolation by distance with restricted gene flow between neighbouring rivers, which suggests an important homing behaviour. 2. Despite these populations suffering a serious demographic decline during 1998, we did not detect any reduction in their genetic variation, suggesting a reasonably high effective population size and temporal stability. 3. Genetic differences among rivers should be taken into account in future management activities. Given the high genetic variability and the temporal stability observed, we believe that no supportive breeding programmes are presently needed in these populations. [ABSTRACT FROM AUTHOR]

Recent progress in biology and microscopy has made it possible to acquire multidimensional data on rapid cellular activities. Unfortunately, the data analysis needed to describe the observed biological process still remains a major bottleneck. We here present a novel method of studying membrane trafficking by monitoring vesicular structures moving along a three-dimensional cytoskeleton network. It allows the dynamics of such structures to be qualitatively and quantitatively investigated. Our tracking method uses kymogram analysis to extract the consistent part of the temporal information and to allow the meaningful representation of vesicle dynamics. A fully automatic extension of this method, together with a statistical tool for dynamic comparisons, allows the precise analysis and comparison of overall speed distributions and directions. It can handle typical complex situations, such as a dense set of vesicles moving at various velocities, fusing and dissociating with each other or with other cell compartments. The overall approach has been characterized and validated on synthetic data. We chose the Rab6A protein, a GTPase involved in the regulation of intracellular membrane trafficking, as a molecular model. The application of our method to GFP-Rab6A stable cells acquired using fast four-dimensional deconvolution video-microscopy gives considerable cellular dynamic information unreachable using other techniques. [ABSTRACT FROM AUTHOR]

SUMMARY: Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree populations that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree 'Throuba Naxos' was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome‐wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology. Significance Statement: The most comprehensive genomic variation map to date has been developed for olive trees (Olea europaea L. subsp. europaea var. europaea) originating from the entire Mediterranean basin, providing insights into the complex olive tree domestication and biology, and through a selective sweep scan and genome‐wide association approaches candidate genes controlling important agronomic traits in olive tree have been identified. [ABSTRACT FROM AUTHOR]

Copyright of Conservation Biology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

This account presents information on all aspects of the biology of Viscum album L. (Mistletoe) that are relevant to understanding its ecological characteristics and behaviour. The main topics are presented within the standard framework of the Biological Flora of Britain and Ireland: distribution, habitat, communities, responses to biotic factors, responses to environment, structure and physiology, phenology, floral and seed characters, herbivores and disease, history, and conservation.Viscum album is a widespread obligate hemiparasite on a wide range of angiosperm and gymnosperm trees. Once thought to take just water and nutrients from its host via a haustorium, it is now suggested to also take carbon. Heavy infestations can reduce host vitality through prolific water use and carbon removal.Flowers are highly reduced but are primarily pollinated by flies, ants and bees. Seeds are dispersed by birds. Removal of the epicarp is necessary for successful seedling establishment, and seeds have a sticky viscin coat, adhering it to the host bark. Vegetative spread also happens under the bark of its host resulting in densities of >700 Mistletoe plants per host.Viscum album is a lowland species, most frequent in open human‐made habitats extending into woodlands in Europe. It has been widely planted for folklore use centred around Christmas. Despite conservation concerns following removal of Mistletoe‐laden old orchards, the species is thriving and needs control in some areas. Viscotoxins and lectins in leaves and shoots have been widely used in herbal medicine and now potentially in complementary cancer therapy. [ABSTRACT FROM AUTHOR]

Widespread introduced species can be leveraged to investigate the genetic, ecological and adaptive processes underlying rapid evolution and range expansion, particularly the contributions of genetic diversity to adaptation. Rhinella marina, the cane toad, has been a focus of invasion biology for decades in Australia. However, their introduction history in North America is less clear. Here, we investigated the roles of introduction history and genetic diversity in establishment success of cane toads across their introduced range. We used reduced representation sequencing (ddRAD) to obtain 34,000 SNPs from 247 toads in native (French Guiana, Guyana, Ecuador, Panama, Texas) and introduced (Bermuda, southern Florida, northern Florida, Hawaiʻi, Puerto Rico) populations. Unlike all other cane toad introductions, we found that Florida populations were more closely related to native Central American lineages (R. horribilis), than to native Southern American lineages (R. marina). Furthermore, we found high levels of diversity and population structure in the native range, corroborating suggestions that R. marina is a species complex. We also found that introduced populations exhibit only slightly lower genetic diversity than native populations. Together with demographic analyses, this indicates founding populations of toads in Florida were larger than previously reported. Lastly, within R. marina, only one of 245 putatively adaptive SNPs showed fixed differences between native and introduced ranges, suggesting that putative selection in these introduced populations is based upon existing genetic variation. Our findings highlight the importance of genetic sequencing in understanding biological introductions and hint at the role of standing genetic variation in range expansion. [ABSTRACT FROM AUTHOR]

Studying the evolution of genomic divergence between lineages is a topical issue in evolutionary biology. However, the evolutionary forces that shape the heterogeneous divergence of the genomic landscape are still poorly understood. Here, two wind‐pollinated sister‐species (Ostrya japonica and O. chinensis) are used to explore what these potential forces might be. A total of 40 individuals from 16 populations across their main distribution areas in China were sampled for genome‐wide resequencing. Population demography analyses revealed that these two sister‐species diverged at 3.06–4.43 Mya. Both population contraction and increased gene flow were detected during glacial periods, suggesting secondary contact at those times. All three parameters (DXY, π, and ρ) decreased in those regions showing high levels of differentiation (FST). These findings indicate that linked selection and recombination played a key role in the genomic heterogeneous differentiation between the two Ostrya species. Genotype–environment association analyses showed that precipitation was the most important ecological factor for speciation. Such environmentally related genes and positive selection genes may have contributed to local adaptation and the maintenance of species boundaries. [ABSTRACT FROM AUTHOR]

Summary: Centromeres are the genomic regions that organize and regulate chromosome behaviours during cell cycle, and their variations are associated with genome instability, karyotype evolution and speciation in eukaryotes. The highly repetitive and epigenetic nature of centromeres were documented during the past half century. With the aid of rapid expansion in genomic biotechnology tools, the complete sequence and structural organization of several plant and human centromeres were revealed recently. Here, we systematically summarize the current knowledge of centromere biology with regard to the DNA compositions and the histone H3 variant (CENH3)‐dependent centromere establishment and identity. We discuss the roles of centromere to ensure cell division and to maintain the three‐dimensional (3D) genomic architecture in different species. We further highlight the potential applications of manipulating centromeres to generate haploids or to induce polyploids offspring in plant for breeding programs, and of targeting centromeres with CRISPR/Cas for chromosome engineering and speciation. Finally, we also assess the challenges and strategies for de novo design and synthesis of centromeres in plant artificial chromosomes. The biotechnology applications of plant centromeres will be of great potential for the genetic improvement of crops and precise synthetic breeding in the future. [ABSTRACT FROM AUTHOR]

Understanding how populations diverge and new species arise is a central question in evolutionary biology. "Allopatric" divergence through geographical isolation is considered to be the commonest mechanism generating species biodiversity in mountain ecosystems. However, the underlying genomic dynamics, especially genomic islands of elevated divergence and genes that are highly diverged as a result of lineage‐specific selection, remain poorly understood. Stellera chamaejasme has a wide geographical range across the Qinghai–Tibet Plateau and northern China, making it a good model with which to explore genomic divergence during speciation in mountain ecosystems. We assembled a high‐quality, chromosome‐level genome for this species and resequenced the genomes of 24 populations across its major distribution. Our population genomic analyses recovered four distinct genetic lineages corresponding to geographical distributions with contrasting environments. However, we revealed continuous gene flow during the historical divergences of these four lineages. Interlineage hybrids and plastome introgressions were frequently found in regions of contact, which further increased gene flow between two contacting lineages in the recent past. The elevated divergences were highly heterogeneous across the genome and selection of ancestral polymorphisims and divergence hitchhiking contributed greatly to the formation of genomic islands. The highly diverged and lineage‐specific positively selected genes within and outside genomic islands were annotated to be mainly involved in local adaptation. Our results suggest that genomic divergence in S. chamaejasme is likely to have been triggered and maintained by local selection together with geographical isolation. [ABSTRACT FROM AUTHOR]

The adoption of a holistic approach to root research, that is, one that takes into account all categories of root traits, from anatomy to root morphology, physiology and architecture, as well as interactions with the rhizosphere microbiota, was emphasised as a crucial step in facing the challenges posed by global change. Keywords: Ambassador Program; ISRR11; rhizosphere; root phenotyping; root traits; Rooting2021; roots EN Ambassador Program ISRR11 rhizosphere root phenotyping root traits Rooting2021 roots 2149 2154 6 08/22/22 20220915 NES 220915 Emerging frontiers: root and rhizosphere research in the context of global environmental chan... Natural ecosystems and agricultural production have been threatened by multifaceted global environmental changes. ISRR11, rhizosphere, root traits, Ambassador Program, root phenotyping, Rooting2021, roots Root biology never sleeps: 11th Symposium of the International Society of Root Research (ISRR11) and the 9th International Symposium on Root Development (Rooting2021), 24-28 May 2021. [Extracted from the article]

Loss of sexual reproductive capacity has been proposed as a syndrome of domestication in vegetatively propagated crops, but there are relatively few examples from agricultural systems. In this study, we compare sexual reproductive capacity in wild (sexual) and domesticated (vegetative) populations of enset (Ensete ventricosum (Welw.) Cheesman), a tropical banana relative and Ethiopian food security crop.We examined floral and seed morphology and germination ecology across 35 wild and domesticated enset. We surveyed variation in floral and seed traits, including seed weight, viability and internal morphology, and germinated seeds across a range of constant and alternating temperature regimes to characterize optimum germination requirements.We report highly consistent floral allometry, seed viability, internal morphology and days to germination in wild and domesticated enset. However, seeds from domesticated plants responded to cooler temperatures with greater diurnal range. Shifts in germination behaviour appear concordant with a climatic envelope shift in the domesticated distribution.Our findings provide evidence that sexual reproductive capacity has been maintained despite long‐term near‐exclusive vegetative propagation in domesticated enset. Furthermore, certain traits such as germination behaviour and floral morphology may be under continued selection, presumably through rare sexually reproductive events. Compared to sexually propagated crops banked as seeds, vegetative crop diversity is typically conserved in living collections that are more costly and insecure. Improved understanding of sexual propagation in vegetative crops may have applications in germplasm conservation and plant breeding. [ABSTRACT FROM AUTHOR]

Global change encompasses many co‐occurring anthropogenic stressors. Understanding the interactions between these multiple stressors, whether they be additive, antagonistic or synergistic, is critical for ecosystem managers when prioritizing which stressors to mitigate in the face of global change. While such interactions between stressors appear prevalent, it remains unclear if and how these interactions change over time, as the majority of multiple‐stressor studies rarely span multiple generations of study organisms. Although meta‐analyses have reported some intriguing temporal trends in stressor interactions, for example that synergism may take time to emerge, the mechanistic basis for such observations is unknown. In this study, by analysing data from an evolution experiment with the rotifer Brachionus calyciflorus (~35 generations and 31,320 observations), we show that adaptation to multiple stressors shifts stressor interactions towards synergism. We show that trade‐offs, where populations cannot optimally perform multiple tasks (i.e. adapting to multiple stressors), generate this bias towards synergism. We also show that removal of stressors from evolved populations does not necessarily increase fitness and that there is variation in the evolutionary trajectories of populations that experienced the same stressor regimes. Our results highlight outstanding questions at the interface between evolution and global change biology, and illustrate the importance of considering rapid adaptation when managing or restoring ecosystems subjected to multiple stressors under global change. [ABSTRACT FROM AUTHOR]

The sea lamprey (Petromyzon marinus) is an invasive species in the Great Lakes and the focus of a large control and assessment program. Current assessment methods provide information on the census size of spawning adult sea lamprey in a small number of streams, but information characterizing reproductive success of spawning adults is rarely available. We used RAD‐capture sequencing to genotype single nucleotide polymorphism (SNP) loci for ~1600 sea lamprey larvae collected from three streams in northern Michigan (Black Mallard, Pigeon, and Ocqueoc Rivers). Larval genotypes were used to reconstruct family pedigrees, which were combined with Gaussian mixture analyses to identify larval age classes for estimation of spawning population size. Two complementary estimates of effective breeding size (Nb), as well as the extrapolated minimum number of spawners (Ns), were also generated for each cohort. Reconstructed pedigrees highlighted inaccuracies of cohort assignments from traditionally used mixture analyses. However, combining genotype‐based pedigree information with length‐at‐age assignment of cohort membership greatly improved cohort identification accuracy. Population estimates across all three streams sampled in this study indicate a small number of successfully spawning adults when barriers were in operation, implying that barriers limited adult spawning numbers but were not completely effective at blocking access to spawning habitats. Thus, the large numbers of larvae present in sampled systems were a poor indicator of spawning adult abundance. Overall, pedigree‐based Nb and Ns estimates provide a promising and rapid assessment tool for sea lamprey and other species. [ABSTRACT FROM AUTHOR]

In the south-western United States and Mexico, mountain sheep were found to have low levels of mtDNA sequence divergence among haplotypes and low overall nucleotide diversity. Potential causes for this low diversity are discussed. Significant differences in mtDNA haplotype distributions over short distances and high values of NsT on a local scale appear to be a result of the tendency of female mountain sheep to disperse less frequently and over shorter distances than males. A lack of concordance between mtDNA haplotype distributions and assumed subspecies boundaries suggest that some taxonomic labels need to be revised. [ABSTRACT FROM AUTHOR]

The environmental consequences of using nonrenewable fossil fuels have motivated a global quest for sustainable alternatives from renewable sources. Carinata has been developed as a low carbon intensity, non‐food oilseed biomolecular platform to produce advanced drop‐in renewable fuels, meal, and co‐products. The crop is widely adaptable to grow in the humid subtropical and humid continental climatic regions of Asia, Africa, North America, South America, Europe, and Australia as a spring or winter crop. Carinata is heat tolerant, resistant to diseases and seed shattering with lower water‐use requirements than other oilseed brassicas. Adopting carinata in double‐cropping systems would require continuing research to integrate crop biology with agronomy, to understand growth and development and its interaction with agricultural inputs and management. Site‐specific best management agronomic practices and crop improvement research to develop frost‐tolerant, early‐maturing, nutrient use‐efficient, and high yielding varieties with desirable oil content and fatty acid profile will enhance the crop's adaptability and economic viability. The exploitation of intra‐ and interspecific and intra‐ and intergeneric diversity will further enhance carinata productivity and resistance to biotic and abiotic stresses. This review attempts to present a comprehensive description of carinata's biology, beginning with its origin and current state of distribution, availability of genetic and genomic resources, and a discussion of its morphology, phenology, and reproduction. A detailed analysis of the agronomy of the crop, including planting and germination and management practices, is presented in the context of crop growth and development. This will facilitate global adoption, sustainable production, and commercialization of carinata as a dedicated biofuel oilseed crop in diverse cropping systems and growing regions of the world, including the Southeast United States. [ABSTRACT FROM AUTHOR]

Targeted therapies have reshaped the landscape of the development of cancer therapeutics. Recent biomarker‐driven, tissue‐agnostic clinical trials represent a significant paradigm shift in precision cancer medicine. Despite their growth in preclinical and clinical studies, to date only a few biomarker‐driven, tissue‐agnostic indications have seen approval by the US Food and Drug Administration (FDA). These approvals include pembrolizumab in microsatellite instability‐high or mismatch repair deficient solid tumors, as well as both larotrectinib and entrectinib in NTRK fusion‐positive tumors. Complex cancer biology, clinical trial design, and identification of resistance mechanisms represent some of the challenges that future tissue‐agnostic therapies have to overcome. In this Review, we present a brief history of the development of tissue‐agnostic therapies, comparing the similarities in the approval of pembrolizumab, larotrectinib, and entrectinib for tissue‐agnostic indications. We also explore the future of tissue‐agnostic cancer therapeutics while identifying important challenges for the future that drugs targeting tissue‐agnostic indications will face. [ABSTRACT FROM AUTHOR]

Objective: Transgenic re‐expression enables unbiased investigation of T‐cell receptor (TCR)‐intrinsic characteristics detached from its original cellular context. Recent advancements in TCR repertoire sequencing and development of protocols for direct cloning of full TCRαβ constructs now facilitate large‐scale transgenic TCR re‐expression. Together, this offers unprecedented opportunities for the screening of TCRs for basic research as well as clinical use. However, the functional characterisation of re‐expressed TCRs is still a complicated and laborious matter. Here, we propose a Jurkat‐based triple parameter TCR signalling reporter endogenous TCR knockout cellular platform (TPRKO) that offers an unbiased, easy read‐out of TCR functionality and facilitates high‐throughput screening approaches. Methods: As a proof‐of‐concept, we transgenically re‐expressed 59 human cytomegalovirus‐specific TCRs and systematically investigated and compared TCR function in TPRKO cells versus primary human T cells. Results: We demonstrate that the TPRKO cell line facilitates antigen‐HLA specificity screening via sensitive peptide‐MHC‐multimer staining, which was highly comparable to primary T cells. Also, TCR functional avidity in TPRKO cells was strongly correlating to primary T cells, especially in the absence of CD8αβ co‐receptor. Conclusion: Overall, our data show that the TPRKO cell lines can serve as a surrogate of primary human T cells for standardised and high‐throughput investigation of TCR biology. [ABSTRACT FROM AUTHOR]

Summary: Expression reprogramming directed by transcription factors is a primary gene regulation underlying most aspects of the biology of any organism. Our views of how gene regulation is coordinated are dramatically changing thanks to the advent and constant improvement of high‐throughput profiling and transcriptional network inference methods: from activities of individual genes to functional interactions across genes. These technical and analytical advances can reveal the topology of transcriptional networks in which hundreds of genes are hierarchically regulated by multiple transcription factors at systems level. Here we review the state of the art of experimental and computational methods used in plant biology research to obtain large‐scale datasets and model transcriptional networks. Examples of direct use of these network models and perspectives on their limitations and future directions are also discussed. Significance Statement: Understanding gene function is a critical requirement to advance knowledge of the principles underpinning fundamental and applied plant biology. In this review, we describe predictive analyses, their strengths and pitfalls that are fast‐forwarding our understanding of gene regulation and function in plants. [ABSTRACT FROM AUTHOR]

Understanding the origin of new species is a central goal in evolutionary biology. Diverging lineages often evolve highly heterogeneous patterns of genetic differentiation; however, the underlying mechanisms are not well understood. We investigated evolutionary processes governing genetic differentiation between the hybridizing campions Silene dioica (L.) Clairv. and S. latifolia Poiret. Demographic modelling indicated that the two species diverged with gene flow. The best‐supported scenario with heterogeneity in both migration rate and effective population size suggested that a small proportion of the loci evolved without gene flow. Differentiation (FST) and sequence divergence (dXY) were correlated and both tended to peak in the middle of most linkage groups, consistent with reduced gene flow at highly differentiated loci. Highly differentiated loci further exhibited signatures of selection. In between‐species population pairs, isolation by distance was stronger for genomic regions with low between‐species differentiation than for highly differentiated regions that may contain barrier loci. Moreover, differentiation landscapes within and between species were only weakly correlated, suggesting that linked selection due to shared recombination and gene density landscapes is not the dominant determinant of genetic differentiation in these lineages. Instead, our results suggest that divergent selection shaped the genomic landscape of differentiation between the two Silene species, consistent with predictions for speciation in the face of gene flow. [ABSTRACT FROM AUTHOR]

Control of bovine viral diarrhea virus (BVDV) in cattle populations across most of the world has remained elusive in spite of advances in knowledge about this viral pathogen. A central feature of virus perseverance in cattle herds is the unique mechanism of persistent infection. Managing BVDV infection in herds involves controlling persistently infected carrier animals using a multidimensional approach of vaccination, biosecurity, and identification of BVDV reservoirs. A decade has passed since the original American College of Veterinary Internal Medicine consensus statement on BVDV. While much has remained the same with respect to clinical signs of disease, pathogenesis of infection including persistent infection, and diagnosis, scientific articles published since 2010 have led to a greater understanding of difficulties associated with control of BVDV. This consensus statement update on BVDV presents greater focus on topics currently relevant to the biology and control of this viral pathogen of cattle, including changes in virus subpopulations, infection in heterologous hosts, immunosuppression, and vaccination. [ABSTRACT FROM AUTHOR]

Ambient temperature modulates reproductive processes, especially in poikilotherms such as teleosts. Consequently, global warming is expected to impact the reproductive function of fish, which has implications for wild population dynamics, fisheries and aquaculture. In this extensive review spanning tropical and cold‐water environments, we examine the impact of higher‐than‐optimal temperatures on teleost reproductive development and physiology across reproductive stages, species, generations and sexes. In doing so, we demonstrate that warmer‐than‐optimal temperatures can affect every stage of reproductive development from puberty through to the act of spawning, and these responses are mediated by age at spawning and are associated with changes in physiology at multiple levels of the brain–pituitary–gonad axis. Response to temperature is often species‐specific and changes with environmental history/transgenerational conditioning, and the amplitude, timing and duration of thermal exposure within a generation. Thermally driven changes to physiology, gamete development and maturation typically culminate in poor sperm and oocyte quality, and/or advancement/delay/inhibition of ovulation/spermiation and spawning. Although the field of teleost reproduction and temperature is advanced in many respects, we identify areas where research is lacking, especially for males and egg quality from "omics" perspectives. Climate‐driven warming will continue to disturb teleost reproductive performance and therefore guide future research, especially in the emerging areas of transgenerational acclimation and epigenetic studies, which will help to understand and project climate change impacts on wild populations and could also have implications for aquaculture. [ABSTRACT FROM AUTHOR]

Cercospora leaf spot, caused by the fungal pathogen Cercospora beticola, is the most destructive foliar disease of sugar beet worldwide. This review discusses C. beticola genetics, genomics, and biology and summarizes our current understanding of the molecular interactions that occur between C. beticola and its sugar beet host. We highlight the known virulence arsenal of C. beticola as well as its ability to overcome currently used disease management strategies. Finally, we discuss future prospects for the study and management of C. beticola infections in the context of newly employed molecular tools to uncover additional information regarding the biology of this pathogen. Taxonomy: Cercospora beticola Sacc.; Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Capnodiales, Family Mycosphaerellaceae, Genus Cercospora. Host range: Well‐known pathogen of sugar beet (Beta vulgaris subsp. vulgaris) and most species of the Beta genus. Reported as pathogenic on other members of the Chenopodiaceae (e.g., lamb's quarters, spinach) as well as members of the Acanthaceae (e.g., bear's breeches), Apiaceae (e.g., Apium), Asteraceae (e.g., chrysanthemum, lettuce, safflower), Brassicaceae (e.g., wild mustard), Malvaceae (e.g., Malva), Plumbaginaceae (e.g., Limonium), and Polygonaceae (e.g., broad‐leaved dock) families. Disease symptoms: Leaves infected with C. beticola exhibit circular lesions that are coloured tan to grey in the centre and are often delimited by tan‐brown to reddish‐purple rings. As disease progresses, spots can coalesce to form larger necrotic areas, causing severely infected leaves to wither and die. At the centre of these spots are black spore‐bearing structures (pseudostromata). Older leaves often show symptoms first and younger leaves become infected as the disease progresses. Management: Application of a mixture of fungicides with different modes of action is currently performed although elevated resistance has been documented in most employed fungicide classes. Breeding for high‐yielding cultivars with improved host resistance is an ongoing effort and prudent cultural practices, such as crop rotation, weed host management, and cultivation to reduce infested residue levels, are widely used to manage disease. Useful website: https://www.ncbi.nlm.nih.gov/genome/11237?genome_assembly_id=352037 [ABSTRACT FROM AUTHOR]

The field of ion mobility mass spectrometry (IM‐MS) has developed rapidly in recent decades, with new fundamental advances underpinning innovative applications. This has been particularly noticeable in the field of biomacromolecular structure determination and structural biology, with pioneering studies revealing new structural insight for complex protein assemblies which control biological function. This perspective offers a review of recent developments in IM‐MS which have enabled expanding applications in protein structural biology, principally focusing on the quantitative measurement of collision cross sections and their interpretation to describe higher order protein structures. [ABSTRACT FROM AUTHOR]

Peanut is one of the most common food triggers of fatal anaphylaxis worldwide although peanut allergy affects only 1%‐2% of the general population. Peanuts are the source of highly potent allergenic proteins. It is emerging that the allergenicity of certain proteins is linked to their biological function. Peanut is an unusual crop in that it flowers aboveground but produces its seed‐containing pods underground. This so‐called geocarpic fruiting habit exposes pods and seeds during their development to soilborne pathogens and pests. Pest damage can also open routes of entry for opportunistic fungi such as Aspergillus. Although seed proteins have primary functions in nutrient reservoirs, lipid storage bodies, or the cytoskeleton, they have also evolved to act as part of the plant's defense system to enhance fitness and survival of the species. When interacting with pathogens or pests, these proteins modify and damage cells' membranes, interact with immune receptors, and modulate signaling pathways. Moreover, following exposure, the immune system of predisposed individuals reacts to these proteins with the production of specific IgE. This review explores the evolutionary biology of peanut and its seed proteins and highlights possible links between the proteins' biological function and their allergenicity. [ABSTRACT FROM AUTHOR]

Aromatic compounds, which are traditionally derived from petroleum feedstocks, represent a diverse class of molecules with a wide range of industrial and commercial applications. Significant progress has been made to alternatively and sustainably produce many aromatics from renewable substrates using microbial biocatalysts. While the construction of both natural and non‐natural pathways has expanded the number and diversity of aromatic bioproducts, pathway modularization in both single‐ and multi‐strain systems continues to support the enhancement of key production metrics towards economically‐viable levels. Emerging tools for implementing more precise metabolic control (e.g. CRISPRi, sRNA) as well as the engineering of novel high‐throughput screening platforms utilizing in vivo aromatic biosensors, meanwhile, continue to facilitate further optimization of both pathways and hosts. While product toxicity persists as a key challenge limiting the production of many aromatics, various successful strategies have been demonstrated towards improving tolerance, including via membrane and efflux pump engineering as well as by exploiting alternative production hosts. Finally, as a further step towards sustainable and economical aromatic bioproduction, non‐model substrates including lignin‐derived compounds continue to emerge as viable feedstocks. This review highlights recent and notable achievements related to such efforts while offering future outlooks towards engineering microbial cell factories for aromatic production. © 2018 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Abstract: This year marks the 50th anniversary of Monte B. Lloyd's “Mean Crowding” (1967) paper, in which he introduced a metric that accounts for an individual's experience of conspecific density. Mean crowding allows ecologists to measure the degree of spatial aggregation of individuals in a manner relevant to intraspecific competition for resources. We take the concept of mean crowding a step beyond its most common usage and that it has a mathematical relationship to many of the most important concepts in ecology and evolutionary biology. Mean crowding, a first‐order approximation of the degree of nonrandomness in a distribution, can function as a powerful heuristic that can unify concepts across disciplines in a more general way that Lloyd originally envisioned. [ABSTRACT FROM AUTHOR]

Summary: Ubiquitination is mediated by an enzymatic cascade that results in the modification of substrate proteins, redefining their fate. This post‐translational modification is involved in most cellular processes, yet its analysis faces manifold obstacles due to its complex and ubiquitous nature. Reconstitution of the ubiquitination cascade in bacterial systems circumvents several of these problems and was shown to faithfully recapitulate the process. Here, we present UbiGate − a synthetic biology toolbox, together with an inducible bacterial expression system – to enable the straightforward reconstitution of the ubiquitination cascades of different organisms in Escherichia coli by ‘Golden Gate’ cloning. This inclusive toolbox uses a hierarchical modular cloning system to assemble complex DNA molecules encoding the multiple genetic elements of the ubiquitination cascade in a predefined order, to generate polycistronic operons for expression. We demonstrate the efficiency of UbiGate in generating a variety of expression elements to reconstitute autoubiquitination by different E3 ligases and the modification of their substrates, as well as its usefulness for dissecting the process in a time‐ and cost‐effective manner. [ABSTRACT FROM AUTHOR]

Weedy rice ( Oryza spp.), a weedy relative of cultivated rice ( O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the 'agricultural weed syndrome', making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties ( aus and indica) and wild rice. Moreover, the two main groups of weedy rice in the USA, which are also related to aus and indica cultivars, constitute a separate origin from that of Asian weeds. Weedy rice populations in South Asia largely converge on presence of red pericarps and awns and on ease of shattering. Genomewide divergence scans between weed groups from the USA and South Asia, and their crop relatives are enriched for loci involved in metabolic processes. Some candidate genes related to iconic weedy traits and competitiveness are highly divergent between some weed-crop pairs, but are not shared among all weed-crop comparisons. Our results show that weedy rice is an extreme example of recurrent evolution, and suggest that most populations are evolving their weedy traits through different genetic mechanisms. [ABSTRACT FROM AUTHOR]

Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over-hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random-bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well-differentiated clusters (average ФST = 0.159, Rst = 0.392, P > 0.001; Analysis of molecular variance [ AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild-living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average ФST = 0.103, Rst = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north-eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene-early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free-ranging domestic cats along corridor edges should be carefully monitored. [ABSTRACT FROM AUTHOR]

The article offers brief profile of behavioral ecologist Joanna Burger, who grew up on a farm in Niskayuna, New York, and studied biology in her graduation. Topics discussed include her role in influencing ecological risk analyst for improving human and ecological health, improvement of human and ecological health, and conserving and understanding of society.

Virtually nothing in nature is uniform. Observed at the right scale, most entities are clustered rather than evenly distributed, spatially and temporally, and this applies across domains from the distribution of matter in the universe, to habitats across the Earth's surface, and to energy in the landscape. Patchiness means organisms cannot carve out even territories. Instead, their shape and size depends on the dispersion of materials needed for survival and reproduction. This fundamental feature of life is intrinsically understood in ecology, for example, in the ideal free distribution and optimal foraging theory, and is represented in the anatomy as well as behaviour of organisms via the structures and strategies for moving, finding and capturing these patchy resources. But perhaps most striking of all is the role of patchiness in facilitating the formation of social groups - of societies. The resource dispersion hypothesis ( RDH) suggests that where resources are dispersed and rich enough, multiple individuals can collapse into groups that share the same space at little cost to each other. Cooperation may be absent, but sociality is favoured nevertheless. Thirty years after the origin of the hypothesis, we review the accumulating models, critiques, evidence and experiments, concluding that RDH is a pervasive feature of animal spacing patterns across a wide range of species, taxonomic groups and ecosystems. In the spirit of the original objective of the Huxley Reviews to 'suggest and inspire research that will improve our knowledge in the future', we also take the opportunity to consider wider implications of the RDH. If we live and evolved on a patchwork planet, then we should expect broader effects. Indeed, we suggest that the RDH has played an important role in the evolution of cooperation, biodiversity, behaviour and, not least, in the social organization of humans in our evolutionary past and today. [ABSTRACT FROM AUTHOR]

Miniature inverted repeat transposable elements (MITEs) are the most ubiquitous transposable elements in eukaryotic genomes; they play a prominent role in sequence divergence and genome evolution. There are many well-characterized Stowaway-like MITE families in wheat, but their distribution, abundance, and composition at the chromosome level are still not well understood. In this study, we systematically investigated the Stowaway-like MITEs in wheat group 7 chromosomes based on the survey sequences of isolated wheat chromosomes, to compare them at the chromosome level and to reveal their evolutionary role on wheat polyploidization. In summary, 2026 MITEs were identified, of which 587, 714, and 725 were distributed on 7A, 7B, and 7D chromosomes, respectively. There are more MITEs present on 7D, compared to 7A and 7B, suggesting A and B subgenomes eliminated some repetitive elements during two hybridization processes. Furthermore, some chromosome/arm-specific MITEs were also identified, providing information on the function and evolution of MITEs in wheat genomes. The sequence diversity of the MITE insertions was also investigated. This study for the first time investigated the abundance and composition of MITEs at the chromosome level, which will be beneficial to improve our understanding of the distribution of wheat MITEs and their evolutionary role in polyploidization. [ABSTRACT FROM AUTHOR]

The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a crop's range of cultivation into environments that are more extreme than those in which it was domesticated, including into "sustainable" agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings. [ABSTRACT FROM AUTHOR]

Calorespirometric measurements of metabolic heat rates and CO2 emission rates of respiring tissues as functions of temperature enable rapid determination of the temperatures that plants are adapted to without growing them in different environmental temperatures. However, the correct choice of target material for measurements that enable prediction of growth temperature responses is crucial, and needs to be identified in a species- and trait-specific manner. In this study, different carrot materials were tested: a primary culture system proposed as an in vitro test system for carrot yield potential, taproots of young plants, and the root meristem of actively growing plants during secondary root growth. The central root meristem is the most suitable for studying temperature response by calorespirometry for genotype comparison. Calorespirometric methods for predicting genotype-specific temperature responses of crop plant cultivars can be used to predict productivity in environments with differing temperature conditions. [ABSTRACT FROM AUTHOR]