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Background: Forage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker – trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS). Results: Using 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length. Conclusion: FarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security. [ABSTRACT FROM AUTHOR]

Abstract Background Forage sorghum is a highly valued crop in livestock feed production due to its versatility, adaptability, high productivity, and resilience under adverse environmental conditions, making it a crucial option for sustainable forage production. This study aimed to investigate ninety-five forage sorghum genotypes and identify the marker – trait associations (MTAs) in adaptive traits, including yield and flowering through genome-wide association studies (GWAS). Results Using 41,854 polymorphic SNPs, a GWAS involving the GLM, MLM, and FarmCPU models was performed to analyse fourteen adaptive traits. The population structure revealed the presence of two subpopulation groups. Linkage disequilibrium (LD) plots showed varying degrees of LD decay across the chromosomes, with an average LD decay of 19.49 kbp. Twelve common significant QTNs, encoding 17 putative candidate genes, were simultaneously co-detected and studied by at least two or more GWAS methods. Three QTNs were associated to days to 50% flowering; two each to leaf-to-stem ratio and number of nodes per plant; and one each to plant height, leaf width, number of leaves per plant, stem girth, and internodal length. Six candidate genes were associated with days to 50% flowering, two each with leaf width, stem girth, leaf-to-stem ratio, and number of nodes per plant, and one each with plant height, number of leaves per plant, and internodal length. Conclusion FarmCPU was identified as the most suitable and effective among all the models for controlling both false positives and false negatives. Further in-depth analysis of the newly discovered QTNs may lead to the identification of new candidate genes for the trait of interest. These studies elucidate gene functions and could transform forage sorghum breeding through marker-assisted selection and transgenic approaches, accelerating the development of superior forage sorghum varieties and enhancing global food security.

The multipurpose tree Neltuma alba is widely distributed in forests of north-central Argentina but overexploitation and deforestation have led to forest transformation and endangered genetic diversity of this species. Thus, developing germplasm management strategies for the conservation and use of the species is crucial. In this context, the availability of georeferenced ecogeographic information along with multivariate analysis techniques facilitates the characterisation, classification and prediction of adaptive patterns, providing a framework for decision-making. In the present study, an Ecogeographic Land Characterisation (ELC) map was generated to assess the ecogeographic representativeness of N. alba germplasm collections and design seed transfer zones (STZs). Adaptive trait data recorded for different plant materials from several provenances across the species’ range in Argentina were used to validate the methodology. The germplasm collections were ecogeographically representative of the occurrence observed; however, some ecogeographic gaps were identified. Of the 45 ecogeographical categories generated in the ELC map, 12 provisional STZs were established. The STZs showed consensus with the morphological groups generated using adaptive traits. This study demonstrates the usefulness of ecogeographic analyses as a preliminary tool to develop strategies for the collection and use of native plant genetic resources. Furthermore, the validation of models with genetic data ensures their effectiveness for restoration and/or afforestation activities. [ABSTRACT FROM AUTHOR]

Most of the attention given to intraspecific crop, livestock, and aquaculture diversity in agricultural production systems has been targeted at their roles in providing provisioning services, such as food and fibre or their cultural services, providing non-material benefits, such as places for recreation and inspiration. The additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services for agricultural productivity and ecosystem resilience has been largely neglected. A literature review was carried out across sectors (crop, livestock, aquaculture), both on the counterfactual, i.e., the lack of intraspecific diversity in the production system and on the direct and indirect roles that intraspecific diversity plays in maintaining seven of the regulating and supporting ecosystem services: (i) regulating pest and diseases; (ii) maintaining and regulating water and soil quality; (iii) regulating and improving the flow of reproductive diversity; (iv) buffering excess or lack of water; (v) regulating soil erosion; (vi) nutrient cycling in water and soil; and (vii) supporting habitat maintenance. Benefits from the use of intraspecific diversity, diversity per se, and adaptive traits include a limited use of chemical inputs and unsustainable practices and their negative impact on livelihoods, ecosystem functioning, and productivity. All sectors (crop, livestock, and aquaculture) should be examined in the agricultural production system to understand the provision of the different ecosystem services by intraspecific diversity. Differences in structure, functioning, and temporal and spatial scales of these sectors should also be considered. Supporting and regulating ecosystem services often have relatively longer-term processes than food provisioning and rely not only on the current diversity but also on its presence over time. The presented regulating and supporting ecosystem services rely on the presence of the diversity from the farm to the landscape and to agroecological zone. Neglecting the additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services is shown in this review to be detrimental to agricultural productivity and landscape resilience. [ABSTRACT FROM AUTHOR]

The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) to detect the new loci, including the heading date (HD), maturating date (MD), plant height (PH), and lodging resistance (LR). In total, 41 loci existing in all 21 chromosomes, except for 4A and 6B, were identified, and each explained 4.3–18.9% of the phenotypic variations existing in two or more environments. Of these, 13 loci are overlapped with the known genes or quantitative trait loci (QTLs), whereas the other 28 are likely to be novel. The 1A locus (296.9–297.7 Mb) is a multi-effect locus for LR and PH, whereas the locus on chromosome 6D (464.5–471.0 Mb) affects both the HD and MD. Furthermore, four candidate genes for adaptive traits were identified, involved in cell division, signal transduction, and plant development. Additionally, two competitive, allele-specific PCR (KASP) markers, Kasp_2D_PH for PH and Kasp_6D_HD for HD, were developed and validated in another 162 spring wheat accessions. Our study uncovered the genetic basis of adaptive traits and provided the associated SNPs and varieties with more favorable alleles for wheat MAS breeding. [ABSTRACT FROM AUTHOR]

The contribution of genetic adaptation and plasticity to intraspecific phenotypic variability remains insufficiently studied in long‐lived plants, as well as the relevance of neutral versus adaptive processes determining such divergence. We examined the importance of phylogeographic structure and climate in modulating genetic and plastic changes and their interdependence in fitness‐related traits of a widespread Mediterranean conifer (Pinus pinaster). Four marker‐based, previously defined neutral classifications along with two ad hoc climate‐based categorizations of 123 range‐wide populations were analyzed for their capacity to summarize genetic and plastic effects of height growth and survival (age 20) in 15 common gardens. The plasticity of tree height and differential survival were interpreted through mixed modeling accounting for heteroscedasticity in the genotype‐by‐environment dataset. The analysis revealed a slight superiority of phylogeographic classifications over climate categorizations on the explanation of genetic and plastic effects, which suggests that neutral processes can be at least as important as isolation by climate as a driving factor of evolutionary divergence in a prevalent pine. The best phylogeographic classification involved eight geographically discrete genetic groups, which explained 92% (height) and 52% (survival) of phenotypic variability, including between‐group mean differentiation and differential expression across trials. For height growth, there was high predictability of plastic group responses described by different reaction norm slopes, which were unrelated to between‐group mean differentiation. The latter differences (amounting to ca. 40% among groups) dominated intraspecific performance across trials. Local adaptation was evident for genetic groups tested in their native environments in terms of tree height and, especially, survival. This finding was supported by QST > FST estimates. Additionally, our range‐wide evaluation did not support a general adaptive syndrome by which less reactive groups to ameliorated conditions would be associated with high survival and low growth. In fact, a lack of relationship between mean group differentiation, indicative of genetic adaptation, and predictable group plasticity for height growth suggests different evolutionary trajectories of these mechanisms of phenotypic divergence. Altogether, the existence of predictable adaptive‐trait phenotypic variation for the species, involving both genetic differentiation and plastic effects, should facilitate integrating genomics and environment into decision‐making tools to assist forests in coping with climate change. [ABSTRACT FROM AUTHOR]

Most of the attention given to intraspecific crop, livestock, and aquaculture diversity in agricultural production systems has been targeted at their roles in providing provisioning services, such as food and fibre or their cultural services, providing non-material benefits, such as places for recreation and inspiration. The additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services for agricultural productivity and ecosystem resilience has been largely neglected. A literature review was carried out across sectors (crop, livestock, aquaculture), both on the counterfactual, i.e., the lack of intraspecific diversity in the production system and on the direct and indirect roles that intraspecific diversity plays in maintaining seven of the regulating and supporting ecosystem services: (i) regulating pest and diseases; (ii) maintaining and regulating water and soil quality; (iii) regulating and improving the flow of reproductive diversity; (iv) buffering excess or lack of water; (v) regulating soil erosion; (vi) nutrient cycling in water and soil; and (vii) supporting habitat maintenance. Benefits from the use of intraspecific diversity, diversity per se, and adaptive traits include a limited use of chemical inputs and unsustainable practices and their negative impact on livelihoods, ecosystem functioning, and productivity. All sectors (crop, livestock, and aquaculture) should be examined in the agricultural production system to understand the provision of the different ecosystem services by intraspecific diversity. Differences in structure, functioning, and temporal and spatial scales of these sectors should also be considered. Supporting and regulating ecosystem services often have relatively longer-term processes than food provisioning and rely not only on the current diversity but also on its presence over time. The presented regulating and supporting ecosystem services rely on the presence of the diversity from the farm to the landscape and to agroecological zone. Neglecting the additional role that intraspecific crop, livestock, and aquaculture diversity has in providing regulating and supporting ecosystem services is shown in this review to be detrimental to agricultural productivity and landscape resilience.

Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries’ adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima’s D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries’ adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome.

Abstract Background Spiders comprise a hyperdiverse lineage of predators with venom systems, yet the origin of functionally novel spider venom glands remains unclear. Previous studies have hypothesized that spider venom glands originated from salivary glands or evolved from silk-producing glands present in early chelicerates. However, there is insufficient molecular evidence to indicate similarity among them. Here, we provide comparative analyses of genome and transcriptome data from various lineages of spiders and other arthropods to advance our understanding of spider venom gland evolution. Results We generated a chromosome-level genome assembly of a model spider species, the common house spider (Parasteatoda tepidariorum). Module preservation, GO semantic similarity, and differentially upregulated gene similarity analyses demonstrated a lower similarity in gene expressions between the venom glands and salivary glands compared to the silk glands, which questions the validity of the salivary gland origin hypothesis but unexpectedly prefers to support the ancestral silk gland origin hypothesis. The conserved core network in the venom and silk glands was mainly correlated with transcription regulation, protein modification, transport, and signal transduction pathways. At the genetic level, we found that many genes in the venom gland-specific transcription modules show positive selection and upregulated expressions, suggesting that genetic variation plays an important role in the evolution of venom glands. Conclusions This research implies the unique origin and evolutionary path of spider venom glands and provides a basis for understanding the diverse molecular characteristics of venom systems.

Research assessing the relationship of the five-factor model (FFM) to personality disorder symptomatology has generally been confirmatory, with three exceptions. The exceptions have been failures to confirm associations of conscientiousness with the obsessive-compulsive personality disorder, agreeableness with dependent, and openness with schizotypal. Haigler and Widiger demonstrated empirically years ago that this was occurring because the predominant FFM measure at that time, the NEO Personality Inventory–Revised, does not include a sufficient representation of maladaptive variants of the respective FFM personality trait domains. Research since their study has continued to fail to confirm the FFM hypotheses, using other measures of the FFM. The current study extended the work of Haigler and Widiger by considering three additional FFM measures, the Big Five Inventory–2 (BFI-2), the International Item Pool–NEO-120 (IPIP-NEO-120), and the Inventory of Personal Characteristics–5 (IPC-5). Data were obtained from a community sample of adults with experience of mental health treatment. The results confirmed an improvement in the FFM–personality disorder relationships when the experimentally manipulated versions of the BFI-2, IPIP-NEO-120, and IPC-5 were used. The implications of the findings for existing and future FFM–personality disorder research are discussed. [ABSTRACT FROM AUTHOR]

Alien species are a significant threat to natural ecosystems and human economies. Despite global efforts to address this challenge, the documented number of alien species is rapidly increasing worldwide. However, the magnitude of the impact of alien species may vary significantly across habitats. For example, some habitats are naturally less prone to biological invasions due to stringent abiotic and biotic characteristics, selecting for a limited number of introduced species possessing traits closely related to the native organisms. Subterranean ecosystems are quintessential examples of habitats with strong environmental filters (e.g. lack of light and scarcity of food), driving convergent adaptations in species that have successfully adapted to life in darkness. Despite these stringent environmental constraints, the number of records of alien species in subterranean ecosystems has increased in recent decades, but the relevant literature remains largely fragmented and mostly anecdotal. Therefore, even though caves are generally considered very fragile ecosystems, their susceptibility to impacts by alien species remains untested other than for some very specific cases. We provide the first systematic literature survey to synthesise available knowledge on alien species in subterranean ecosystems globally. This review is supported by a database summarising the available literature, aiming to identify gaps in the distribution and spread of alien invertebrate species in subterranean habitats, and laying the foundations for future management practices and interventions. First, we quantitatively assessed the current knowledge of alien species in subterranean ecosystems to shed light on broader questions about taxonomic biases, geographical patterns, modes of dispersal, pathways for introductions and potential impacts. Secondly, we collected species‐specific traits for each recorded alien species and tested whether subterranean habitats act as ecological filters for their establishment, favouring organisms with pre‐adaptive traits suitable for subterranean life. We found information on the presence of 246 subterranean alien species belonging to 18 different classes. The dominant alien species were invertebrates, especially insects and arachnids. Most species were reported in terrestrial subterranean habitats from all continents except Antarctica. Palaearctic and Nearctic biogeographic regions represented the main source of alien species. The main routes of introductions into the recipient country are linked to commercial activities (84.3% of cases for which there was information available). Negative impacts have been documented for a small number of case studies (22.7%), mostly related to increased competition with native species. For a limited number of case studies (6.1%), management strategies were reported but the effectiveness of these interventions has rarely been quantified. Accordingly, information on costs is very limited. Approximately half of the species in our database can be considered established in subterranean habitats. According to our results, the presence of suitable traits grants access to the stringent environmental filter posed by subterranean environments, facilitating establishment in the new habitat. We recommend that future studies deepen the understanding of invasiveness into subterranean habitats, raising public and scientific community awareness of preserving these fragile ecosystems. [ABSTRACT FROM AUTHOR]

Background: Spiders comprise a hyperdiverse lineage of predators with venom systems, yet the origin of functionally novel spider venom glands remains unclear. Previous studies have hypothesized that spider venom glands originated from salivary glands or evolved from silk-producing glands present in early chelicerates. However, there is insufficient molecular evidence to indicate similarity among them. Here, we provide comparative analyses of genome and transcriptome data from various lineages of spiders and other arthropods to advance our understanding of spider venom gland evolution. Results: We generated a chromosome-level genome assembly of a model spider species, the common house spider (Parasteatoda tepidariorum). Module preservation, GO semantic similarity, and differentially upregulated gene similarity analyses demonstrated a lower similarity in gene expressions between the venom glands and salivary glands compared to the silk glands, which questions the validity of the salivary gland origin hypothesis but unexpectedly prefers to support the ancestral silk gland origin hypothesis. The conserved core network in the venom and silk glands was mainly correlated with transcription regulation, protein modification, transport, and signal transduction pathways. At the genetic level, we found that many genes in the venom gland-specific transcription modules show positive selection and upregulated expressions, suggesting that genetic variation plays an important role in the evolution of venom glands. Conclusions: This research implies the unique origin and evolutionary path of spider venom glands and provides a basis for understanding the diverse molecular characteristics of venom systems. [ABSTRACT FROM AUTHOR]

The dissection of the genetic architecture and the detection of the loci for adaptive traits are important for marker-assisted selection (MAS) for breeding. A spring wheat diversity panel with 251 cultivars, mainly from China, was obtained to conduct a genome-wide association study (GWAS) to detect the new loci, including the heading date (HD), maturating date (MD), plant height (PH), and lodging resistance (LR). In total, 41 loci existing in all 21 chromosomes, except for 4A and 6B, were identified, and each explained 4.3–18.9% of the phenotypic variations existing in two or more environments. Of these, 13 loci are overlapped with the known genes or quantitative trait loci (QTLs), whereas the other 28 are likely to be novel. The 1A locus (296.9–297.7 Mb) is a multi-effect locus for LR and PH, whereas the locus on chromosome 6D (464.5–471.0 Mb) affects both the HD and MD. Furthermore, four candidate genes for adaptive traits were identified, involved in cell division, signal transduction, and plant development. Additionally, two competitive, allele-specific PCR (KASP) markers, Kasp_2D_PH for PH and Kasp_6D_HD for HD, were developed and validated in another 162 spring wheat accessions. Our study uncovered the genetic basis of adaptive traits and provided the associated SNPs and varieties with more favorable alleles for wheat MAS breeding.

Societal Impact Statement The productivity of sorghum in Ethiopia has been largely limited by rain‐fed conditions because farmers tend to use local drought‐tolerant but low‐yielding landraces, as high‐yielding and late‐maturing landrace cultivars risk failure due to drought. Addressing such issues often requires a far‐reaching approach to identify and incorporate new traits into a gene pool, followed by a period of selection to re‐establish an overall adaptive phenotype. The sorghum backcross nested association mapping (BC‐NAM) population developed in this study increases the genetic diversity available in Ethiopian elite adapted sorghum germplasm, providing new scope to improve food security in a region known for periodic devastating droughts. Summary As the center of diversity for sorghum, Sorghum bicolor (L.) Moench, elite cultivars selected in Ethiopia are of central importance to sub‐Saharan food security. Despite being presumably well adapted to their center of diversity, elite Ethiopian sorghums nonetheless experience constraints to productivity, for example, associated with shifting rainfall patterns associated with climate change. A sorghum backcross nested association mapping (BC‐NAM) population developed by crossing 13 diverse lines pre‐identified to have various drought resilience mechanisms with an Ethiopian elite cultivar, Teshale, was tested under three rain‐fed environments in Ethiopia. Twenty‐seven, 15, and 15 quantitative trait loci (QTLs) with predominantly small additive effects were identified for days to flowering, days to maturity, and plant height, respectively. Many associations detected in this study corresponded closely to known or candidate genes or previously mapped QTLs, supporting their validity. The expectation that genotypes such as Teshale from the center of diversity tend to have a history of strong balancing selection, with novel variations more likely to persist in small marginal populations, was strongly supported in that for these three traits, nearly equal numbers of alleles from the donor lines conferred increases and decreases in phenotype relative to the Teshale allele. Such rich variation provides a foundation for selection to arrive at a new “adaptive peak,” exemplifying the nature of efforts that may be necessary to adapt many crops to new climate extremes.

Simple Summary: In this study, we investigated whether predation pressures in the early life history of frogs can result in an anuran-affect behavior response in the later stages of their life history. Tadpoles that undergo predation pressure possess smaller body sizes, slower development rates, and broader caudal fins. In particular, juvenile frogs that undergo predation pressure from the tadpole stage also metamorphosize later, develop longer limbs, narrower skulls, and demonstrate other finer changes in the skeleton of the lower body. On this note, we predicted that this would change the locomotory performance of such juvenile frogs in terms of their swimming and jumping speed, but such an eventuality did not take place. It appears, then, that predation pressure in the early life history of frogs does not alter their jumping and swimming speed abilities. Moreover, such a fact suggests that this morphological change may not be a predator-adaptive response. Anuran species can respond to environmental changes via phenotypic plasticity, which can also result in ecological impacts across the life history of such species. We investigated the effects of predation pressure (i.e., the non-consumption effect) from the dragonfly larva (Anax parthenope) on the phenotypical change of tadpoles into juvenile frogs (specifically the black-spotted pond frog, Pelophylax nigromaculatus), and also analyzed the impact of morphological changes on locomotory performance after metamorphosis. The experiments on predator impact were conducted in the laboratory. Body length, weight, development timing, and metamorphosis timing in the presence of dragonfly nymphs were measured in both tadpoles and juvenile frogs. The body and tail shapes of the tadpoles, as well as the skeletal shape of the juvenile frogs, were analyzed using landmark-based geometric morphometrics. Furthermore, the locomotory performance of the juvenile frogs was tested by measuring their jumping and swimming speeds. Tadpoles that had grown with predators possessed smaller bodies, deeper tail fins, and slower development rates, and they waited longer periods of time before commencing metamorphosis. Having said this, however, the effect of predator cues on the body length and weight of juvenile frogs was not found to be significant. These juvenile frogs possessed longer limbs and narrower skulls, with subtle morphological changes in the pelvis and ilium, but there was no subsequent difference in their swimming and jumping speeds. Our results showed that the changes in anatomical traits that can affect locomotor performance are so subtle that they do not affect the jumping or swimming speeds. Therefore, we support the view that these morphological changes are thus by-products of an altered tadpole period, rather than an adaptive response to predator-escape ability or to post-metamorphosis life history. On the other hand, delayed metamorphosis, without an increase in body size, may still be disadvantageous to the reproduction, growth, and survival of frogs in their life history following metamorphosis. [ABSTRACT FROM AUTHOR]

Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is an invasive pest species that uses a wide variety of commercial fruit as a breeding and feeding resource. The damage to the fruit generated by D. suzukii´ oviposition causes considerable economic losses. Therefore, the maintenance of D. suzukii in the lab conditions constitutes a fundamental tool for research proposal. Two of the determining factors affecting the lab rearing conditions are the culture medium and density. In this study, we evaluated the impact of these factors on three components associated with fitness: development time, larval-adult viability and body size, comparing the effects of three culture media: cornmeal (polenta), mashed potato and plum when the flies were reared at three densities: 10, 30 and 50 larvae per 5ml of culture medium. Our results revealed that the flies reared the cornmeal culture medium and at lower densities provide the better conditions for the maintenance of D. suzukii under lab conditions. [ABSTRACT FROM AUTHOR]

Woody perennial angiosperms (i.e., hardwood trees) are polyphyletic in origin and occur in most angiosperm orders. Despite their independent origins, hardwoods have shared physiological, anatomical, and life history traits distinct from their herbaceous relatives. New high-throughput DNA sequencing platforms have provided access to numerous woody plant genomes beyond the early reference genomes of Populus and Eucalyptus, references that now include willow and oak, with pecan and chestnut soon to follow. Genomic studies within these diverse and undomesticated species have successfully linked genes to ecological, physiological, and developmental traits directly. Moreover, comparative genomic approaches are providing insights into speciation events while large-scale DNA resequencing of native collections is identifying population-level genetic diversity responsible for variation in key woody plant biology across and within species. Current research is focused on developing genomic prediction models for breeding, defining speciation and local adaptation, detecting and characterizing somatic mutations, revealing the mechanisms of gender determination and flowering, and application of systems biology approaches to model complex regulatory networks underlying quantitative traits. Emerging technologies such as single-molecule, long-read sequencing is being employed as additional woody plant species, and genotypes within species, are sequenced, thus enabling a comparative ("evo-devo") approach to understanding the unique biology of large woody plants. Resource availability, current genomic and genetic applications, new discoveries and predicted future developments are illustrated and discussed for poplar, eucalyptus, willow, oak, chestnut, and pecan.

The phyllosphere (i.e., the aerial parts of plants) harbors a rich microbial life, including bacteria, fungi, viruses, and yeasts. Current knowledge of yeasts stems primarily from industrial and medical research on Saccharomyces cerevisiae and Candida albicans , both of which can be found on plant tissues. For most other yeasts found in the phyllosphere, little is known about their ecology and functions. Here, we explore the diversity, dynamics, interactions, and genomics of yeasts associated with plant leaves and how tools and approaches developed for model yeasts can be adopted to disentangle the ecology and natural functions of phyllosphere yeasts. A first genomic survey exemplifies that we have only scratched the surface of the largely unexplored functional potential of phyllosphere yeasts. The plant microbiome has received enormous attention over the past decade and a wealth of knowledge has been obtained on the diversity and functions of bacteria, fungi, protists, and, to some extent, viruses. Several plant-associated microorganisms have a pivotal role in plant growth and health by modulating plant physiology, development, and tolerance to (a)biotic stresses. To date, most phyllosphere microbiome studies have focused on bacteria and filamentous fungi, with little known about yeasts living on and inside aerial plant parts. Yeasts have diverse adaptive traits to cope with the harsh conditions in the phyllosphere, such as biofilm formation, carbon and nitrogen acquisition, and the production of pigments and killer toxins. However, their genetic and genomic diversity and mechanisms involved in their spatiotemporal dynamics and interactions with other phyllosphere members remain largely elusive. [ABSTRACT FROM AUTHOR]

Sorghum ( Sorghum bicolor ) is a significant crop serving food, energy, feed, and industrial raw materials, featuring extensive growth adaptability and diverse utility values. Despite the achievements in sorghum breeding in the last decades, conventional breeding methods still confront challenges such as lengthy breeding cycles, low efficiency, and complex genetic backgrounds. With the rapid advancement of molecular biology, genetics, and bioinformatics, molecular breeding has carved new pathways for enhancing sorghum yield and quality. This article reviews the molecular basic research progress in the key agronomic and adaptive traits of sorghum, including grain yield, grain quality, flowering time, plant height, tillering, stress resistance, and male sterility, and discusses future research priorities, offering novel insights and approaches for sorghum breeding.

Abstract Background Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. Results A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. Conclusions The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

Drought challenges crop production worldwide. The issue is aggravated by frequent drought episodes and unpredictable rainfall patterns associated with global climate change. While the efforts to breed drought-resistant crop varieties are progressing, the need of the hour is immediate strategies to sustain the yields of existing ones. As per recent studies, stress adaptive traits can be activated using specific elicitors. Endophytes that inhabit host plants asymptomatically are natural elicitors/bio-stimulators capable of activating host gene expression, conferring several benefits to the hosts. This review discusses the scope of using trait-specific endophytes in activating drought adaptive traits in crop varieties.

Societal Impact Statement: The productivity of sorghum in Ethiopia has been largely limited by rain‐fed conditions because farmers tend to use local drought‐tolerant but low‐yielding landraces, as high‐yielding and late‐maturing landrace cultivars risk failure due to drought. Addressing such issues often requires a far‐reaching approach to identify and incorporate new traits into a gene pool, followed by a period of selection to re‐establish an overall adaptive phenotype. The sorghum backcross nested association mapping (BC‐NAM) population developed in this study increases the genetic diversity available in Ethiopian elite adapted sorghum germplasm, providing new scope to improve food security in a region known for periodic devastating droughts. Summary: As the center of diversity for sorghum, Sorghum bicolor (L.) Moench, elite cultivars selected in Ethiopia are of central importance to sub‐Saharan food security. Despite being presumably well adapted to their center of diversity, elite Ethiopian sorghums nonetheless experience constraints to productivity, for example, associated with shifting rainfall patterns associated with climate change.A sorghum backcross nested association mapping (BC‐NAM) population developed by crossing 13 diverse lines pre‐identified to have various drought resilience mechanisms with an Ethiopian elite cultivar, Teshale, was tested under three rain‐fed environments in Ethiopia.Twenty‐seven, 15, and 15 quantitative trait loci (QTLs) with predominantly small additive effects were identified for days to flowering, days to maturity, and plant height, respectively. Many associations detected in this study corresponded closely to known or candidate genes or previously mapped QTLs, supporting their validity.The expectation that genotypes such as Teshale from the center of diversity tend to have a history of strong balancing selection, with novel variations more likely to persist in small marginal populations, was strongly supported in that for these three traits, nearly equal numbers of alleles from the donor lines conferred increases and decreases in phenotype relative to the Teshale allele. Such rich variation provides a foundation for selection to arrive at a new "adaptive peak," exemplifying the nature of efforts that may be necessary to adapt many crops to new climate extremes. [ABSTRACT FROM AUTHOR]

BackgroundModern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited.ResultsWe sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres.ConclusionsWe uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the "wild ancestor" of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

'Caviano' is a black bean cultivar recommended for Santa Catarina, for being highly adaptable to the main grain-producing regions of the state (mean grain yield 2315 kg ha-1). Compared to previously released cultivars, Caviano has a larger root system and desirable characteristics for mechanical harvesting. [ABSTRACT FROM AUTHOR]

Promiscuous plasmids like IncP-1 plasmids play an important role in the bacterial adaptation to pollution by acquiring and distributing xenobiotic catabolic genes. However, most information comes from isolates and the role of plasmids in governing community-wide bacterial adaptation to xenobiotics and other adaptive forces is not fully understood. Current information on the contribution of IncP-1 plasmids in community adaptation is limited because methods are lacking that directly isolate and identify the plasmid borne adaptive functions in whole-community DNA. In this study, we optimized long-range PCR to directly access and identify the cargo carried by IncP-1 plasmids in environmental DNA. The DNA between the IncP-1 backbone genes trbP and traC, a main insertion site of adaptive trait determinants, is amplified and its content analyzed by high-throughput sequencing. The method was applied to DNA of an onfarm biopurification system (BPS), treating pesticide contaminated wastewater, to examine whether horizontal gene exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. The cargo recovered from BPS community DNA encoded catabolic but also resistance traits and various other (un)known functions. Unexpectedly, genes with catabolic traits composed only a minor fraction of the cargo, indicating that the IncP-1 region between trbP and traC is not a major contributor to catabolic adaptation of the BPS microbiome. Instead, it contains a functionally diverse set of genes which either may assist biodegradation functions, be remnants of random gene recruitment, or confer other crucial functions for proliferation in the BPS environment. IMPORTANCE This study presents a long-range PCR for direct and cultivation-independent access to the identity of the cargo of a major insertion hot spot of adaptive genes in IncP-1 plasmids and hence a new mobilome tool for understanding the role of IncP-1 plasmids in complex communities. The method was applied to DNA of an on-farm biopurification system (BPS) treating pesticide-contaminated wastewater, aiming at new insights on whether horizontal exchange of catabolic functions by IncP-1 plasmids is a main driver of community adaptation in BPS. Unexpectedly, catabolic functions represented a small fraction of the cargo genes while multiple other gene functions were recovered. These results show that the cargo of the target insertion hot spot in IncP-1 plasmids in a community, not necessarily relates to the main obvious selective trait imposed on that community. Instead, these functions might contribute to adaptation to unknown selective forces or represent remnants of random gene recruitment. [ABSTRACT FROM AUTHOR]

The commonly observed negative relationship between stomatal density (SD) and atmospheric CO2 has led to SD being proposed as an indicator of atmospheric CO2 concentration. The use of SD as a proxy for CO2, however, has been hampered by an insufficient understanding of the intraspecific variation of this trait. We hypothesized that SD in Pinus sylvestris, a widely distributed conifer, varies geographically and that this variation is determined by major climatic variables. By sampling needles from naturally growing trees along a latitudinal range of 32.25°, equivalent to 13.7°C gradient of mean annual temperature (MAT) across Europe, we found that SD decreased from the warmest southern sites to the coldest sites in the north at a rate of 4 stomata per mm2 for each 1°C, with MAT explaining 44% of the variation. Additionally, samples from a provenance trial exhibited a positive relationship between SD and the MAT of the original localities, suggesting that high SD is an adaptation to warm temperature. Our study revealed one of the strongest intraspecific relationships between SD and climate in any woody species, supporting the utility of SD as a temperature, rather than direct CO2, proxy. In addition, our results predict the response of SD to climate warming. We showed that mean annual temperature is a major positive driver of stomatal density (SD) in Pinus sylvestris needles, both in samples collected across its European range and in a common‐garden trial. This finding suggests that SD may be used as a temperature indicator in climatic research and allows to predict the response of SD to climate warming. [ABSTRACT FROM AUTHOR]

Anuran species can respond to environmental changes via phenotypic plasticity, which can also result in ecological impacts across the life history of such species. We investigated the effects of predation pressure (i.e., the non-consumption effect) from the dragonfly larva (Anax parthenope) on the phenotypical change of tadpoles into juvenile frogs (specifically the black-spotted pond frog, Pelophylax nigromaculatus), and also analyzed the impact of morphological changes on locomotory performance after metamorphosis. The experiments on predator impact were conducted in the laboratory. Body length, weight, development timing, and metamorphosis timing in the presence of dragonfly nymphs were measured in both tadpoles and juvenile frogs. The body and tail shapes of the tadpoles, as well as the skeletal shape of the juvenile frogs, were analyzed using landmark-based geometric morphometrics. Furthermore, the locomotory performance of the juvenile frogs was tested by measuring their jumping and swimming speeds. Tadpoles that had grown with predators possessed smaller bodies, deeper tail fins, and slower development rates, and they waited longer periods of time before commencing metamorphosis. Having said this, however, the effect of predator cues on the body length and weight of juvenile frogs was not found to be significant. These juvenile frogs possessed longer limbs and narrower skulls, with subtle morphological changes in the pelvis and ilium, but there was no subsequent difference in their swimming and jumping speeds. Our results showed that the changes in anatomical traits that can affect locomotor performance are so subtle that they do not affect the jumping or swimming speeds. Therefore, we support the view that these morphological changes are thus by-products of an altered tadpole period, rather than an adaptive response to predator-escape ability or to post-metamorphosis life history. On the other hand, delayed metamorphosis, without an increase in body size, may still be disadvantageous to the reproduction, growth, and survival of frogs in their life history following metamorphosis.

Background: Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties. Results: A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome. Conclusions: The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change. [ABSTRACT FROM AUTHOR]

Traits are the primary attributes that distinguish a species niche. Species and higher taxa are part of a structured phylogeny, and variation in plant traits depends on lineage as well as on environmental conditions. Therefore, it is crucial to investigate linkages between taxonomic identity, shared ancestry, and environment for understanding the variation in leaf traits. We investigated the evolutionary relationships, based on multiple gene sequences among 26 plant species sampled along an elevational gradient from 650 to 3600 m a.s.l. in the central Himalaya. We tested for the phylogenetic signal based on three different measures in 10 leaf traits having a significant association with the resource acquisition-conservation trade-offs axis and influencing plant growth, development, and ecological performance. We further assessed the role of elevation and growth forms as the potential drivers of leaf traits variation while controlling for phylogeny. 5 out of 10 leaf traits showed significant phylogenetic signal. Plant species clustered more often by growth forms at the tips of the phylogeny indicating multiple instances of independent evolution. Evergreen taxa showed niche separation with deciduous and incorporated larger trait variation. Trait variations were guided by both growth forms and elevation when accounted for phylogeny. Growth form has a higher contribution to trait variation compared to elevation. Trade-offs were detected between resource conservation and resource acquisition machinery traits (that would maximise carbon gain), differing between growth forms and along elevation. [ABSTRACT FROM AUTHOR]

Partnerships between researchers and restoration practitioners can improve restoration outcomes, which is especially important for restoration in challenging settings. Here, we describe one such partnership in the Great Basin, United States, which used trait‐based methods and practitioner knowledge to identify the most promising seed sources for restoration. Managers in this region can either use widely available commercial seeds, which are often sourced from far outside the seeding area, or take extra steps to use locally collected seeds. We asked whether local, wild‐collected seeds of two native plants, Elymus elymoides and Poa secunda, had traits more conducive to seedling establishment in degraded sites, relative to commercial sources. Seeds were collected from four remnant native populations within lands managed by the Winnemucca Bureau of Land Management. Collections were screened for seed and seedling characteristics previously identified as associated with increased seedling performance in degraded Great Basin systems, and we provide a detailed methodology for these measurements. Relative to commercial seeds, wild‐collected seeds had more characteristics identified as beneficial for seedling establishment, including phenology, root allocation, root form, and overall size characteristics that suggest locally sourced populations would be likely to establish better than commercial sources. Using phenotypic traits as criteria, the most promising wild populations were selected for agronomic production to increase the quantities of seeds available for restoration, and field trials are ongoing using these field‐increased seeds. These results provide support for collaborative efforts to identify, collect, screen, and increase the availability of local seed sources to improve restoration success. [ABSTRACT FROM AUTHOR]

Context: Evaluation of the performance of dairy cows kept in different production systems is essential for the development of appropriate breeding strategies. Aims: To examine milk production and reproductive performance of crossbred (CB) and indigenous (I) dairy cows, farmers' traits preference for CB and I breeding females, and factors affecting the performance of dairy cattle on smallholdings in selected towns of Jimma Zone, Ethiopia. Methods: In total, 52 smallholder dairy cattle farmers were randomly sampled and data were collected through individual face-to-face interviews by using structured questionnaires. The traits studied were daily milk yield (DMY), lactation milk yield (LMY), lactation length (LL), age at first service (AFS), age at first calving (AFC), calving interval (CI), days open (DO), and number of service per conception (NSC), all being factors affecting performance of dairy cattle and farmers' preferred dairy traits. Results: On average, CB cows had significantly (P < 0.05) higher DMY (6.0 ± 0.33 vs 1.8 ± 0.07 L/cow), LMY (1466.7 ± 1.13 vs 376.0 ± 21.02 L (L)), LL (8.1 ± 0.41 vs 6.9 ± 0.22 months), and lower AFS (2.69 ± 0.1 vs 3.3 ± 0.07 years), AFC (3.7 ± 0.13 vs 4.3 ± 0.07 years) and CI (21.2 ± 1.37 vs 29.8 ± 1.30 months) than did I cows. However, DO and NSC were not significantly (P > 0.05) affected by genotype. In order of perceived importance, high milk yield (mean rank = 0.306), LL (0.292) and fertility (0.199) were farmers' most preferred traits for CB breeding cows, and the corresponding preferred traits for I cows were high milk yield (0.253), adaptability (0.229) and LL (0.192). The most important factors perceived by farmers affecting the performance of dairy cattle were breed, nutrition, diseases, breeding and management practices Conclusions: The findings of the study indicated that even though CB cows performed better, the performance of both breeds of dairy cows in the study area was found to be generally low due to delayed AFS, late AFC, long CI, shorter LL, low daily and LMY and high NSC. Implications: The study highlighted that there is a potential for increasing the performance of dairy cows in the study area, through improved management strategies leading to shorter AFS, AFC, CI and lower NSC. Furthermore, future breed-improvement programs should take into consideration farmers' trait preferences in design of sustainable improvement programs. In Ethiopia, smallholder urban and per-urban dairy farming contributes to improve the welfare of farm households through income generation, providing a source of food and employment. However, there is limited information on productive and reproductive performance of dairy cows, farmers' trait preferences of breeding cows and factors affecting the performance of cows in the study area; the present study addressed this information gap. The findings of the study will provide valuable information for the development of appropriate breeding goals to facilitate genetic improvement of dairy cattle in the study area. [ABSTRACT FROM AUTHOR]

Seasonality, rather than annual precipitation levels, is expected to affect the adaptive responses of plant populations under future climate change. To estimate adaptive traits’ variation, we conducted a common garden experiment with two beech populations from contrasting climatic origins (Evros with longer drought intervals during summer and higher precipitation seasonality, and Drama representing a more temperate ecosystem). We simulated two different watering treatments (frequent vs. non-frequent) on beech seedlings, according to predicted monthly precipitation levels expected to prevail in 2050 by the CSIRO MK3.6 SRESA1B model, considering as reference area a natural beech stand in Mt. Rodopi, Greece. A series of morphological and stem anatomical traits were measured. Seedling survival was greater for the Evros population compared to that of Drama under non-frequent watering, while no difference in survival was detected under frequent watering. Leaf morphological traits were not generally affected by watering frequency except for leaf circularity, which was found to be lower under non-frequent watering for both populations. Stomata density in leaves was found to be higher in the Evros population and lower in the Drama population under non-frequent watering than frequent. Stem anatomical traits were higher under non-frequent watering for Evros but lower for the Drama population. Multivariate analyses clearly discriminated populations under non-frequent rather than frequent watering, indicating genetic adaptation to the population’s environment of origin.

Abstract Background The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits often show strong local adaptation along environmental gradients but, despite their importance, the genetic architecture of these traits remains poorly understood. Results We integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations. Conclusions Our results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.

A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to perform the same function, that is, produce and deliver a cocktail of potent molecules to subdue prey or predators. Venomous organisms therefore offer unique opportunities to investigate the evolutionary processes of convergence of key adaptive traits, and the molecular mechanisms underlying the emergence of novel genes, cells, and tissues. Indeed, some venomous species have already proven to be highly amenable as models for developmental studies, and recent work with venom gland organoids provides manipulatable systems for directly testing important evolutionary questions. Here, we provide a synthesis of the current knowledge that could serve as a starting point for the establishment of venom systems as new models for evolutionary and molecular biology. In particular, we highlight the potential of various venomous species for the study of cell differentiation and cell identity, and the regulatory dynamics of rapidly evolving, highly expressed, tissue-specific, gene paralogs. We hope that this review will encourage researchers to look beyond traditional study organisms and consider venom systems as useful tools to explore evolutionary novelties. [ABSTRACT FROM AUTHOR]

Ants are a widespread group of ecologically important insects. Therefore, ants that are important predators of other ants are likely to play key roles by changing the abundance and impacts of their prey. Familiar arthropod predators, like army ants, are known for their overwhelming raids on invertebrate prey but are limited to mostly tropical systems. Thief ants (Genus: Solenopsis Westwood) are a cosmopolitan group of mostly subterranean ants found in a wide variety of ecosystem types. They are known for their extremely small sizes and their specialized predation where they stealthily tunnel into the nests of other larger ant species to capture and consume only immature ants (larvae and pupae). Predation of ant colonies by other ants, and specialized predatory behaviors of presumed top ant predators (e.g., army ants) are well known. However long‐term predation effects, such as across several seasons, are still poorly understood because of a lack of experimental studies. Here we report results of a ~1.5‐year press field experiment where thief ants were reduced in natural ant communities. Potential impacts, such as predator‐release, were quantified by sampling the co‐occurring ant community. Compared to control plots, overall worker abundance and biomass increased where thief ants were reduced, and effects varied among ant species. Results suggest predator release as select aboveground foraging ant species increased in abundance and that thief ants may act as significant predators. Because thief ants are abundant and widespread, similar predatory effects may occur in many ant communities, and our understanding of important predators may need to adjust to include thieving species as well as army ants. Thief ants are very abundant, tiny, specialized to consume immature life stages, equipped with powerful venom, eusocial, and subterranean. This suite of adaptive traits seems unique to eusocial predators compared to animals, where "thieving" predators are usually larger in size compared to their adult‐sized prey. Future work quantifying top‐down regulation of prey and cascading consumptive and non‐consumptive effects will help to understand thief ant predation and potential effects on ecosystem processes. [ABSTRACT FROM AUTHOR]

Fagus sylvatica in Europe is expected to be severely affected by the ongoing climate change. In this article, seed adaptive traits, in terms of morphology and germination, of F. sylvatica populations of different postglacial lineage and intrapopulation genetic diversity were evaluated. Eight plots from two geographical provenances, Evros and Drama, were selected. Provenance shaped both morphology and germination patterns, but the effect was more pronounced on germination. Seeds from Drama were larger and heavier than those from Evros but exhibited a higher degree of dormancy and slower germination. High among-plots variability on morphology and germination was also observed, especially in Evros. This higher variability was consistent with the higher level of genetic diversity observed at genomic and chloroplast DNA markers at small or larger spatial scales from previous published studies on the same plots. Results suggested the existence of different seed adaptation strategies, mainly between provenances, as a result of possible adaptation to different environmental conditions, whereas a possible influence of a generally complex pattern of admixture between different beech subspecies and postglacial lineages could not be excluded. [ABSTRACT FROM AUTHOR]

Populations that breed along steep elevation gradients show diverse physiological and morphological changes in response to the different environmental conditions. The latter has been discussed by Bergmann's and Allen's ecogeographic rules about body and appendage sizes and environmental temperature. We compared morphometric measures (mass, bill width, tarsus, wing, and tail length) of a Zonotrichia capensis population in two localities at different elevations with similar latitudes and photoperiods on the western slope of the Colombian Central Andes. We compared a Low Elevation locality (LE) at 1800 m a.s.l. and a High Elevation locality (HE) at 3853 m a.s.l. that have approximate wind speeds of 1.3 m/s and 8.4 m/s, respectively. During 12 months of sampling, we captured 46 adults using mist-nets; 26 in the LE and 20 in the HE. Each individual was sexed using molecular techniques at the Laboratory of Genetics of the Department of Biological Sciences of Universidad de Caldas. Individuals (males + females) from the HE had longer wings and tails than those from the LE (F1,44 = 5.93; P = 0.019). Also, wings of males in the HE were longer than those of females in both localities and tails of males in the HE were longer than those of LE males. Our results did not agree with what was expected according to Allen's and Bergmann's ecogeographic rules. Longer wings and tails increase sustainment, maneuverability, and balance in low atmospheric pressures and strong air currents and these conditions are found at high elevation habitats. Most likely, the longer wings found for HE males allow greater movement during territorial behavior. Further, these differences in morphological traits along elevational gradients could result from micro-evolutionary changes between localities or phenotypic plasticity of individuals exposed to different environmental conditions. [ABSTRACT FROM AUTHOR]

• A new conceptual framework on germination niche shaped by hydro-thermal traits. • Key inter-relations between quantitative germination traits for almost 500 species. • Patterns and co-correlants in the cardinal values for species' germination niche. • A database to determine the vegetation boundaries of wild or cultivated species. The germination niche of plant species depends primarily on the seeds' responsiveness to temperature and water potential. However, to appreciate future climate risks to natural regeneration through germination, a global level synthesis across species is needed. We performed a meta-regression and phylogenetic patterning of primary data from 377 studies on 486 species, including trees, grasses, crops and wild species, to determine patterns and co-correlants in the cardinal values that define species' germination niches. We found positive correlations between base temperature and other germination traits related to cardinal temperatures suggesting that plant species alter base temperature values in harmony with other thermal traits as a highly efficient adaptation strategy to coping with harsh conditions. A negative correlation was found between thermal time and base temperature, and positive correlations between other cardinal temperatures and base temperature. Mean values of thermal time indicate that annual crops germinate more rapidly compared to wild species, potentially as a consequence of domestication, and tropical tree seeds the slowest. Dryland species (Cactaceae and Agavaceae) have the widest upper thermal and lower moisture niches, indicative of abilities to grow under harsh conditions, while forages have the narrowest thermal and moisture niches, suggesting higher sensitivity to frost or drought. We propose a new conceptual framework for future research on germination niche as shaped by thermal and moisture traits. Our database represents a unique source of information to further determine the vegetation boundaries of wild or cultivated species, including within simulation studies on plant species adaptations under changing land-use and climate. [ABSTRACT FROM AUTHOR]

Global flooding events are becoming more frequent due to climate change. Depending on the intensity, flooding can cause below-ground plant tissues to become waterlogged and above-ground plant tissues to become partially or fully submerged, leading to hypoxic environments. These conditions can damage plant tissue, leading to chlorosis and senescence, and typically halting plant growth and development, resulting in significant yield loss. Many economically important Brassicaceae crops are susceptible to flooding stress, such as Brassica napus (canola), Brassica oleracea (broccoli, cabbage, Chinese kale), and Brassica rapa (caisin), as well as the Brassicaceae model species Arabidopsis thaliana, which has led to the characterization of physical and molecular responses of these species under flooding. Additionally, comparative studies with native wetland Brassicaceae species, such as species in the Rorripa genus and Nasturtium officinale (watercress), provide insight into phenotypic and genetic adaptive traits to flooded environments. This review reports the current knowledge of morphological, physiological, and molecular responses of Brassicaceae species under flooding stress, highlighting both interspecies and intraspecies comparisons that reveal shared and distinct adaptations and mechanisms involved in flooding responses. We include a discussion of candidate genes with the potential to improve flooding tolerance in Brassicaceae crops and future directions for this field of research. • Brassicaceae contains economically important crops susceptible to flooding damage. • Wetland Brassicaceae species have adaptive traits to mitigate flooding stress. • HRE1 and HRE2 are Brassicaceae ERF-VII genes upregulated under flooding and hypoxia. • Flooding or hypoxia-sensitive Brassicaceae species do not maintain fermentation rates. • Application of Brassicaceae genes underlying flood tolerance can mitigate crop loss. [ABSTRACT FROM AUTHOR]

• Geographical-wise genetic distinction among the dromedary populations was revealed. • Regions under selection were defined on the autosomes of dromedary camels. • Genes related to adaptive physiologies were found within the defined regions. • Haplotype blocks overlapping the candidate regions were defined. • Dromedary genetic diversity and haplotypes under selection need to be conserved. Dromedary camels are a domestic species characterized by various adaptive traits. Limited efforts have been employed toward identifying genetic regions and haplotypes under selection that might be related to such adaptations. These genetic elements are considered valuable sources that should be conserved to maintain the dromedaries' adaptability. Here, we have analyzed whole genome sequences of 40 dromedary camels from different Arabian Peninsula populations to assess their genetic relationship and define regions with signatures of selection. Genetic distinction based on geography was observed, classifying the populations into four groups: (1) North and Central, (2) West, (3) Southwest, and (4) Southeast, with substantial levels of genetic admixture. Using the de-correlated composite of multiple signal approach, which combines four intra-population analyses (Tajima's D index, nucleotide diversity, integrated haplotype score, and number of segregating sites by length), a total of 36 candidate regions harboring 87 genes were identified to be under positive selection. These regions overlapped with 185 haplotype blocks encompassing 1 340 haplotypes, of which 30 (∼2%) were found to be approaching fixation. The defined candidate genes are associated with different biological processes related to the dromedaries' adaptive physiologies, including neurological pathways, musculoskeletal development, fertility, fat distribution, immunity, visual development, and kidney physiology. The results of this study highlight opportunities for further investigations at the whole-genome level to enhance our understanding of the evolutionary pressures shaping the dromedary genome. [ABSTRACT FROM AUTHOR]

Abstract Background Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future.

A phenotype is the expression of interactions between species genotype and environment. We quantified the contributions of ecological and phylogenetic associations to phenotypic variation in Geosmithia fungi. Geosmithia are symbiotic beetle-associated saprotrophs with a range of life histories and host specificities, including obligate nutritional beetle mutualists (ambrosia fungi) and phytopathogens. We hypothesized that: (1) species phenotypes are better explained by their ecology than by their phylogenetic relationships; (2) niche specialization was accompanied by enzymatic capability losses; and (3) ambrosia Geosmithia species have higher nutritional quality and antibiotic capabilities than species with facultative symbioses. Our results confirmed that long-term co-evolved specialists have reduced metabolic breadth in comparison to generalists. Phytopathogenic G. morbida produces unique enzyme suites with affinity to ligno-cellulose. Mycelia of ambrosia fungi contain large amounts of oleic fatty acid with nutritive and possibly allelopathic function. Overall, our results indicate that Geosmithia ecology have greater effect on species phenotype than their phylogenetic relationships. • Enzymatic profiles, biochemical composition and antibiosis in Geosmithia analysed. • Adaptive traits related to the various ecological strategies tracked. • Potential virulence factors of Geosmithia morbida identified. • Specialists exhibit unique enzyme suites and reduced metabolic breadth. • Obligatory symbiotic ambrosia exhibits specific profiles of fatty acids. [ABSTRACT FROM AUTHOR]

In dendritic river systems, gene flow is expected to occur primarily within watersheds. Yet, rare cross‐watershed transfers can also occur, whether mediated by (often historical) geological events or (often contemporary) human activities. We explored these events and their potential evolutionary consequences by analyzing patterns of neutral genetic variation (microsatellites) and adaptive phenotypic variation (male color) in wild guppies (Poecilia reticulata) distributed across two watersheds in northern Trinidad. We found the expected signatures of within‐watershed gene flow; yet we also inferred at least two instances of cross‐watershed gene flow—one in the upstream reaches and one further downstream. The upstream cross‐watershed event appears to be very recent (41 ± 13 years), suggesting dispersal via recent flooding or undocumented human‐mediated transport. The downstream cross‐watershed event appears to be considerably older (577 ± 265 years), suggesting a role for rare geological or climatological events. Alongside these strong signatures of both contemporary and historical gene flow, we found little evidence of impacts on presumably adaptive phenotypic differentiation, except perhaps in the one instance of very recent cross‐watershed gene flow. Selection in this system seems to overpower gene flow—at least on the spatiotemporal scales investigated here. [ABSTRACT FROM AUTHOR]