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Knowledge of global patterns of genetic diversity is essential for biodiversity conservation as this parameter describes the ability of a species to respond to environmental changes. Ichneumonoids parasitoid wasps are among the few taxa showing an anomalous latitudinal diversity gradient. Using the largest georeferenced molecular dataset for this group, we used a macrogenetics approach to examine latitudinal patterns and predictors of intraspecific genetic diversity. We calculated the mean nucleotide diversity of mitochondrial DNA barcode sequences at three geographic levels: grid cells, latitudinal bands and climatic zones. Nucleotide diversity values were consistently higher at northern temperate latitudes, peaking at 50°. We found a positive but weak relationship between intraspecific diversity and the latitude, between intra‐ and interspecific diversity, and a positive effect of the temperature range. Examining the spatial relationship between different levels of biodiversity and its drivers is particularly relevant considering climate change and its impact on species distribution. Yet, in insects, it has been challenging to integrate ecological, evolutionary and geographical components when analysing the processes leading to species richness gradients. [ABSTRACT FROM AUTHOR]

While genetic diversity is theorised to increase the restoration success of degraded plant populations, previous studies examining its impacts on restoration outcomes have yielded mixed results.We hypothesise that the importance of genetic diversity for the performance of plants targeted for restoration increases with environmental stress and varies with specific plant traits related to different plant successive life stages. To test this, we conducted a fully factorial common garden experiment, crossing salinity and genetic diversity under low‐ and high‐nitrogen conditions on the growth and reproduction of Scirpus mariqueter, a threatened endemic saltmarsh plant in the Yangtze Estuary.The impacts of genetic diversity varied across stress gradients and metrics. Under high stress (high salinity, low nutrients), greater diversity enhanced reproductive traits such as clonal growth and seed production, but not under low stress. Plant growth traits showed no diversity effects regardless of stress.Synthesis: Our results highlight the importance of considering intraspecific genetic diversity in ecological restoration and help explain the context‐dependent effects of diversity. [ABSTRACT FROM AUTHOR]

Colletotrichum lindemuthianum is the most frequent pathogenic fungus of the common bean Phaseolus vulgaris. This filamentous fungus employs a hemibiotrophic nutrition/infection strategy, which is characteristic of many Colletotrichum species. Due to host–pathogen coevolution, C. lindemuthianum includes pathotypes with a diversity of virulence against differential common bean varieties. In this study, we performed comparative genomic analyses on three pathotypes with different virulence levels and a non-pathogenic pathotype, isolated from different geographical areas in Mexico. Our results revealed large genomes with high transposable element contents that have undergone expansions, generating intraspecific diversity. All the pathotypes exhibited a similar number of clusters of orthologous genes (COGs) and Gene Ontology (GO) terms. TFomes contain families that are typical in fungal genomes; however, they show different contents between pathotypes, mainly in transcription factors with the fungal-specific TF and Zn2Cys6 domains. Peptidase families mainly contain abundant serine peptidases, metallopeptidases, and cysteine peptidases. In the secretomes, the number of genes differed between the pathotypes, with a high percentage of candidate effectors. Both the virulence gene and CAZyme gene content for each pathotype was abundant and diverse, and the latter was enriched in hemicellulolytic enzymes. We provide new insights into the nature of intraspecific diversity among C. lindemuthianum pathotypes and the origin of their ability to rapidly adapt to genetic changes in its host and environmental conditions. [ABSTRACT FROM AUTHOR]

Phaseolus species are cultivated worldwide as a primary food source for human consumption. Common bean (Phaseolus vulgaris L.) and runner bean (Phaseolus coccineus L.) landraces are often cultivated together. The purpose was to document the traditional knowledge held by farmers regarding bean landraces, to describe the diversity through seed morphological descriptors (five quantitative and five qualitative traits), to understand the geographic distribution using Moran's I statistic, and to analyze the diversity through the Shannon–Wiener Diversity–Equity (H′) index and the Shannon J' homogeneity index at the community level to better understand the richness of this geographic area. A total of 361 common and runner bean accessions were collected in 10 Andean rural communities of Cotacachi, North Ecuador. We identified 47 landraces, predominantly kept by indigenous female farmers, with limited access to formal education, highlighting the role of this disadvantaged population in agrobiodiversity conservation. The cluster analysis revealed three groups (cophenetic correlation coefficient = 0.6). In the principal component (PC) analysis, 94% of the variation was explained by PC1 and PC2. A positive spatial autocorrelation (Moran's I: 0.24; z-score: 2.20; p-value: 0.03) was identified, confirming a spatial structure. The Morochos community showed the highest diversity (H′ = 1.55). The information of the diversity and distribution of common and runner bean variability provided in this study is a contribution to further research focused on conservation. [ABSTRACT FROM AUTHOR]

Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non‐invasive method in biodiversity research, including investigations at the within‐species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode. [ABSTRACT FROM AUTHOR]

The International Union for Conservation of Nature (IUCN) Red List identifies threatened and endangered species and is a key instrument in global biodiversity conservation efforts. Our understanding of the structure and value of genetic biodiversity below the species level is rapidly increasing. Nonetheless, the IUCN assessment criteria overlook genetic variation within species. Here, we address this blind spot and discuss the principles of species conservation status classification relative to intraspecific biodiversity. We focus on coastal species, which thrive in heterogeneous environments known to drive genetic differentiation. The focal example species, Atlantic cod and sugar kelp, have contrasting life histories, are ecologically and economically important constituents of the coastal ecosystem, and are currently not classified as threatened in Norway and Canada. We expose important variation in population structure, the presence of ecotypes and genetic-environment covariation, as well as loss of ecotypes that threatens the conservation of these species. Because the genetic makeup of species directly influences their resilience, omitting this information from conservation status assessments can result in loss of adaptive capacity to future stressors, such as climate change. Consequently, recognizing and preserving intraspecific variation emerges as vital for species' abilities to adapt to and survive in future ocean conditions. [ABSTRACT FROM AUTHOR]

The management of intraspecific diversity in many species is usually disconnected from eco‐evolutionary processes happening in natura. A classic example is embodied in the problem of introgression in hybridized fish populations, wherein management practices are generally unaware of any selective process at work, and therefore generally rely on numbers (adding or removing individuals) to reduce introgression. Such an example can be observed in the French Alps, where native Mediterranea (MED) brown trout have been highly introgressed through decades of stocking with domesticated Atlantic (ATL) brown trout. Recently however, new results shed light on a potential selective mechanism that may affect differentially the fitness of MED and ATL genes depending on the environment (GxE interaction). Using a demogenetic agent‐based model able to account for such GxE interaction, we simulate a management scenario implemented in 2005 by some biodiversity managers and scientists, who attempted to restore the Mediterranea gene pool using translocation of near pure MED individuals in Atlantic‐dominated areas. We show that the model is unable to recreate the observed introgression dynamics if the GxE interaction is not included. This finding implies that (i) eco‐evolutionary mechanisms can have large effects on introgression dynamics on very short time scales and (ii) management of intraspecific diversity should increasingly rely on these natural mechanisms, so as to improve management targets and facilitate adaptation to rapid environmental changes. [ABSTRACT FROM AUTHOR]

Crop homogenization in conventional agriculture has been pervasive while ecology has shown positive effects of biodiversity on ecosystem functioning, that arise from complementarity/facilitation and sampling/selection effects. These effects are well documented for interspecific diversity in both natural ecosystems and agroecosystems but remain less documented at an intraspecific level, particularly for the rates of nutrient uptake by plants and nutrient losses from ecosystems. We conducted a field experiment with 88 experimental plots cultivated with 1, 2, 4 or 8 wheat varieties and 1, 2, 3 or 4 functional groups to assess the effects of the number of varietal and functional diversity of winter wheat on plant biomass production, plant nutrient contents (N, Ca, Cu, Fe, Mg, Mn, P, K, Na and Zn) and fertilizer N recovery in the plant-soil system using a 15N labeling method. We found both negative and positive effects of the number of varieties or number of functional groups on shoot Cu, Fe, Zn, Na and P contents, but no significant effects of intraspecific diversity on biomass production, N content and 15N recovery in the plant-soil system. Our results show differential responses to an increase of intraspecific diversity of wheat on the contents of several essential nutrients in plants and highlight the need to jointly analyze multiple nutrients. Our study also suggests that increasing intraspecific diversity had no overall negative effects on biomass production or N content. Using knowledge on variety functional traits to target specific complementarity mechanisms when designing variety mixtures could thus lead to a positive effect on nutrient absorption and biomass production.

Gracilaria is a genus of major economic interest along the Brazilian coast. Gracilaria caudata is an agarophyte present in different ecoregions of the country. Based on its wide distribution, the intraspecific thermal physiological differentiation across this coast remains uncertain. Thus, we aimed to assess the thermal tolerance of this species and the putative occurrence of ecotypes. To accomplish this, we evaluated the effect of different temperatures (15–35 °C) on growth rates (GRs) and photosynthesis of female gametophytes from four populations along 6,024 km of the Brazilian coast and in three ecoregions: Northeastern (Ceará, CE, 3.23°S), Eastern (Bahia, BA, 12.44°S and Espírito Santo, ES, 20.48°S), as well as Rio Grande (Santa Catarina, SC, 27.11°S). A temperature of 35 ºC was lethal for all populations. BA showed the highest temperature range for survival (15–33 °C) when compared to the others (CE, 18–33 °C; ES, 15–30 °C; SC, 18–30 °C). Temperatures that promoted the highest GRs varied among almost all populations (CE and BA, 23–30 °C; ES, 25–28 °C; SC, 23–28 °C). However, the CE samples had the highest maximal values (12.6 ± 1.4% day−1) and thermal optimum (26.1 ± 0.4 °C) on the thermal performance curve, showing, among all populations, a higher potential for future mariculture tests on the Brazilian coast. Our results show that these populations are ecotypic and that populations from ES and SC may not withstand the predicted increases in seawater temperature, unlike the CE and BA populations, which could withstand temperatures up to 33 °C. [ABSTRACT FROM AUTHOR]

Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis‐related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species. [ABSTRACT FROM AUTHOR]

The five independent countries of Central Asia, namely Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan, contain one of the richest areas in the world for the specific and intraspecific diversity of temperate fruit and nut tree species. Research was carried out via the collaboration of national research and education institutes with local community-based agencies and farmer communities. Raw data (2014 observations) for almond, apple, apricot, cherry plum, currant, grapevine, pear, pomegranate, and walnut were collected at the household (HH) level across the five countries: Uzbekistan, Kazakhstan, Tajikistan, Turkmenistan, and Kyrgyzstan. A set of models was used, including household variety richness as the dependent variable, to understand the influence of socio-ecological variables on the amount and distribution of crop varietal diversity in the farmers' production systems. Four variables were included as explanatory variables of variety richness (fixed factors): ecoregion, ethno-linguistic group, management, and abiotic stress. The results show clear evidence that abiotic stress determines a higher richness of intra-specific diversity in the form of local varieties grown by farmers living in climatically unfavorable areas. The results for the studied ecoregions follow the same trend, with ecoregions with harsher conditions displaying a higher positive correlation with diversity. Mild environments such as the Central Asian riparian woodlands show an unexpectedly lower diversity than other harsher ecoregions. Ethno-linguistic groups also have an effect on the level of varietal diversity used, related to both historic nomadic practices and a culture of harvesting wild fruit and nuts in mountainous areas. The home garden management system hosts a higher diversity compared to larger production systems such as orchards. In Central Asia, encouraging the cultivation of local varieties of fruit and nut trees provides a key productive and resilient livelihood strategy for farmers living under the harsh environmental conditions of the region while providing a unique opportunity to conserve a genetic heritage of global importance. [ABSTRACT FROM AUTHOR]

Intraspecific trait variation (ITV), potentially driven by genetic and non‐genetic mechanisms, can underlie variability in resource acquisition, individual fitness and ecological interactions. Impacts of ITV at higher levels of biological organizations are hence likely, but up‐scaling our knowledge about ITV importance to communities and comparing its relative effects at population and community levels has rarely been investigated.Here, we tested the effects of genetic and non‐genetic ITV on morphological traits in microcosms of protist communities by contrasting the effects of strains showing different ITV levels (i.e. trait averages and variance) on population growth, community composition and biomass production.We found that genetic and non‐genetic ITV can lead to different effects on populations and communities across several generations. Furthermore, the effects of ITV declined across levels of biological organization: ITV directly altered population performance, with cascading but indirect consequences for community composition and biomass productivity.Overall, these results show that the drivers of ITV can have distinct effects on populations and communities, with cascading impacts on higher levels of biological organization that might mediate biodiversity–ecosystem functioning relationships. [ABSTRACT FROM AUTHOR]

• Wheat varietal and functional diversity were manipulated in the field. • Increasing intraspecific diversity of wheat did not influence biomass production. • Increasing intraspecific diversity did not alter 15N recovery by plants and soil. • Increasing intraspecific diversity affected plant Cu, Fe, Zn, Na and P contents. Crop homogenization in conventional agriculture has been pervasive while ecology has shown positive effects of biodiversity on ecosystem functioning, that arise from complementarity/facilitation and sampling/selection effects. These effects are well documented for interspecific diversity in both natural ecosystems and agroecosystems but remain less documented at an intraspecific level, particularly for the rates of nutrient uptake by plants and nutrient losses from ecosystems. We conducted a field experiment with 88 experimental plots cultivated with 1, 2, 4 or 8 wheat varieties and 1, 2, 3 or 4 functional groups to assess the effects of the number of varietal and functional diversity of winter wheat on plant biomass production, plant nutrient contents (N, Ca, Cu, Fe, Mg, Mn, P, K, Na and Zn) and fertilizer N recovery in the plant-soil system using a 15N labeling method. We found both negative and positive effects of the number of varieties or number of functional groups on shoot Cu, Fe, Zn, Na and P contents, but no significant effects of intraspecific diversity on biomass production, N content and 15N recovery in the plant-soil system. Our results show differential responses to an increase of intraspecific diversity of wheat on the contents of several essential nutrients in plants and highlight the need to jointly analyze multiple nutrients. Our study also suggests that increasing intraspecific diversity had no overall negative effects on biomass production or N content. Using knowledge on variety functional traits to target specific complementarity mechanisms when designing variety mixtures could thus lead to a positive effect on nutrient absorption and biomass production. [Display omitted] [ABSTRACT FROM AUTHOR]

Variability of intraspecific host plant quality for phytophagous insects may have consequences on the structure and functioning of associated food webs. The quality of host plants can affect aphids fitness, influencing their life history traits and altering the nutritional resources available to higher trophic levels, potentially affecting the development of solitary parasitoids. Here, we assessed the potential bottom-up effects of intraspecific variability among three cultivars (Gala, Ariane, and Greensleeves) of the domesticated apple tree (Malus domestica) with putative resistance towards the rosy apple aphid (Dysaphis plantaginea) on the aphid's performance, and its cascading effects on the parasitoid Ephedrus cerasicola. We measured aphids pre-reproductive period, lipid, and water contents, and recorded their feeding behavior using the electropenetrography technique. Parasitoid developmental duration, sex ratio, hind tibia size, and female egg load were measured and used to evaluate E. cerasicola performance according to the cultivar on which their aphid hosts had been reared. Only the development time of parasitoids was found to be longer on Ariane and Green Sleeves cultivars than on the Gala cultivar. Aphid-feeding behavior variables related to phloem consumption were negatively impacted on apple tree cultivars on which the development time of parasitoids had been reduced. We discuss ways in which cultivar quality can be an important component of tritrophic interactions: the resistant Ariane and Green Sleeves cultivars negatively impacted the aphids but appeared to have limited bottom-up effects on the parasitoids. [ABSTRACT FROM AUTHOR]

Abstract Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non‐invasive method in biodiversity research, including investigations at the within‐species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode.

The importance of individual nutrients for microbial strain robustness and coexistence in habitats containing different members of the same species is not well understood. To address this for Lactiplantibacillus plantarum in food fermentations, we performed comparative genomics and examined the nutritive requirements and competitive fitness for L. plantarum strains B1.1 and B1.3 isolated from a single sample of teff injera fermentation batter. Compared to B1.1 and other L. plantarum strains, B1.3 has a smaller genome, limited biosynthetic capacities, and large mobilome. Despite these differences, B1.3 was equally competitive with B1.1 in a suspension of teff flour. In commercially sourced, nutrient-replete MRS (cMRS) medium, strain B1.3 reached 3-fold-higher numbers than B1.1 within 2 days of passage. Because B1.3 growth and competitive fitness were poor in mMRS medium (here called mMRS), a modified MRS medium lacking beef extract, we used mMRS to identify nutrients needed for robust B1.3 growth. No improvement was observed when mMRS was supplemented with nucleotides, amino acids, vitamins, or monovalent metals. Remarkably, the addition of divalent metal salts increased the growth rate and cell yields of B1.3 in mMRS. Metal requirements were confirmed by inductively coupled plasma mass spectrometry, showing that total B1.3 intracellular metal concentrations were significantly (up to 2.7-fold) reduced compared to B1.1. Supplemental CaCl2 conferred the greatest effect, resulting in equal growth between B1.1 and B1.3 over five successive passages in mMRS. Moreover, calcium supplementation reversed a B1.3 strain-specific, stationary-phase, flocculation phenotype. These findings show how L. plantarum calcium requirements affect competitive fitness at the strain level. IMPORTANCE Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. Therefore, we investigated two isolates of Lactiplantibacillus plantarum, B1.1 and B1.3, randomly selected from a single batch of teff injera batter. These strains spanned the known genomic and phenotypic range of the L. plantarum species, and in laboratory culture medium used for strain screening, B1.3 exhibited poor growth and was outcompeted by the more robust strain B1.1. Nonetheless, B1.1 and B1.3 were equally competitive in teff flour. This result shows how L. plantarum has adapted for coexistence in that environment. The capacity for the single macronutrient calcium to restore B1.3 competitive fitness in laboratory culture medium suggests that L. plantarum intraspecies diversity found in food systems is fine-tuned to nutrient requirements at the strain level.

The five independent countries of Central Asia, namely Kazakhstan, Kyrgyzstan, Tajikistan, Turkmenistan, and Uzbekistan, contain one of the richest areas in the world for the specific and intraspecific diversity of temperate fruit and nut tree species. Research was carried out via the collaboration of national research and education institutes with local community-based agencies and farmer communities. Raw data (2014 observations) for almond, apple, apricot, cherry plum, currant, grapevine, pear, pomegranate, and walnut were collected at the household (HH) level across the five countries: Uzbekistan, Kazakhstan, Tajikistan, Turkmenistan, and Kyrgyzstan. A set of models was used, including household variety richness as the dependent variable, to understand the influence of socio-ecological variables on the amount and distribution of crop varietal diversity in the farmers’ production systems. Four variables were included as explanatory variables of variety richness (fixed factors): ecoregion, ethno-linguistic group, management, and abiotic stress. The results show clear evidence that abiotic stress determines a higher richness of intra-specific diversity in the form of local varieties grown by farmers living in climatically unfavorable areas. The results for the studied ecoregions follow the same trend, with ecoregions with harsher conditions displaying a higher positive correlation with diversity. Mild environments such as the Central Asian riparian woodlands show an unexpectedly lower diversity than other harsher ecoregions. Ethno-linguistic groups also have an effect on the level of varietal diversity used, related to both historic nomadic practices and a culture of harvesting wild fruit and nuts in mountainous areas. The home garden management system hosts a higher diversity compared to larger production systems such as orchards. In Central Asia, encouraging the cultivation of local varieties of fruit and nut trees provides a key productive and resilient livelihood strategy for farmers living under the harsh environmental conditions of the region while providing a unique opportunity to conserve a genetic heritage of global importance.

Colletotrichum lindemuthianum is the most frequent pathogenic fungus of the common bean Phaseolus vulgaris. This filamentous fungus employs a hemibiotrophic nutrition/infection strategy, which is characteristic of many Colletotrichum species. Due to host–pathogen coevolution, C. lindemuthianum includes pathotypes with a diversity of virulence against differential common bean varieties. In this study, we performed comparative genomic analyses on three pathotypes with different virulence levels and a non-pathogenic pathotype, isolated from different geographical areas in Mexico. Our results revealed large genomes with high transposable element contents that have undergone expansions, generating intraspecific diversity. All the pathotypes exhibited a similar number of clusters of orthologous genes (COGs) and Gene Ontology (GO) terms. TFomes contain families that are typical in fungal genomes; however, they show different contents between pathotypes, mainly in transcription factors with the fungal-specific TF and Zn2Cys6 domains. Peptidase families mainly contain abundant serine peptidases, metallopeptidases, and cysteine peptidases. In the secretomes, the number of genes differed between the pathotypes, with a high percentage of candidate effectors. Both the virulence gene and CAZyme gene content for each pathotype was abundant and diverse, and the latter was enriched in hemicellulolytic enzymes. We provide new insights into the nature of intraspecific diversity among C. lindemuthianum pathotypes and the origin of their ability to rapidly adapt to genetic changes in its host and environmental conditions.

Rapid environmental changes result in massive biodiversity loss, with detrimental consequences for the functioning of ecosystems. Recent studies suggest that intraspecific diversity can contribute to ecosystem functioning to an extent comparable to contributions of interspecific diversity. Knowledge on the relative importance of these two sources of biodiversity is essential for predicting ecosystem consequences of biodiversity loss and will aid in the prioritization of conservation targets and implementation of management measures. However, our quantitative insights into how interspecific and intraspecific biodiversity loss affects ecosystem functioning and how the effects of these two sources of biodiversity loss on ecosystem functioning can be compared are still very limited. To facilitate such quantitative insights, we extend the interspecific Price partitioning method originally introduced by J. Fox in 2006, previously used to quantify species loss and gain effects on ecosystem functioning, to also account for the effects of intraspecific diversity loss and gain on ecosystem function. Using this extended version can yield the quantitative information required for answering research questions addressing correlations between interspecific and intraspecific diversity effects on ecosystem functioning, identifying interspecific and intraspecific groups with large effects, and assessing whether intraspecific diversity can compensate for losses in interspecific diversity. Applying this method to carefully designed experiments will provide additional insights into how biodiversity loss at different ecological levels contributes to and changes ecosystem functioning. [ABSTRACT FROM AUTHOR]

Following the EFSA commodity risk assessment of Malus domestica plants imported from Türkiye into the EU, the EFSA Panel on Plant Health performed a pest categorisation of Pratylenchus loosi (Nematoda: Pratylenchidae) for the EU. Pratylenchus loosi belongs to the order Rhabditida, subfamily Pratylenchidae. This nematode is not known to be present in the EU. The species is not included in the EU Commission Implementing Regulation 2019/2072. The pest occurs primarily in tropical, subtropical and warm temperate areas. It is widely distributed in Asian countries, with tea plants (Camellia sinensis) as the main host. The pest was reported from more than 60 plant species, but reports from hosts other than C. sinensis, e.g. citrus (Citrus spp.) and banana (Musa spp.), are associated with high uncertainty due to doubtful pest identification. Morphological and molecular methods are available for the identification of the pest. Pathways of entry are host plants for planting except seeds, as well as soil attached to plants for planting, machinery or footwear. Soil import to the EU is prohibited from third countries. The climatic preferences of P. loosi are compatible with the microclimatic conditions occurring in the areas of the EU where tea is grown outside. The impact of the nematode is primarily known for Asian countries, where it is a devastating pathogen on tea plants, but there is a key uncertainty on impacts on hosts other than tea. Considering the strong pathogenicity of the pest, its establishment in tea producing areas would have negative consequences for tea producers. Therefore, the Panel concludes that P. loosi satisfies all the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest. [ABSTRACT FROM AUTHOR]

Although numerous studies on the impacts of climate change on biodiversity have been published, only a handful are focused on the intraspecific level or consider population‐level models (separate models per population). We endeavored to fill this knowledge gap relative to the Qinghai‐Tibetan plateau (QTP) by combining species distribution modeling (SDMs) with population genetics (i.e., population‐level models) and phylogenetic methods (i.e., phylogenetic tree reconstruction and phylogenetic diversity analyses). We applied our models to 11 endemic and widely distributed herpetofauna species inhabiting high elevations in the QTP. We aimed to determine the influence of environmental heterogeneity on species' responses to climate change, the magnitude of climate‐change impacts on intraspecific diversity, and the relationship between species range loss and intraspecific diversity losses under 2 shared socioeconomic pathways (SSP245 and SSP585) and 3 future periods (2050s, 2070s, and 2090s). The effects of global climatic change were more pronounced at the intraspecific level (22% of haplotypes lost and 36% of populations lost) than the morphospecies level in the SSP585 climate change scenario. Maintenance of genetic diversity was in general determined by a combination of factors including range changes, species genetic structure, and the part of the range predicted to be lost. This is owing to the fact that the loss and survival of populations were observed in species irrespective of the predicted range changes (contraction or expansion). In the southeast (mountainous regions), climate change had less of an effect on range size (>100% in 3 species) than in central and northern QTP plateau regions (range size <100% in all species). This may be attributed to environmental heterogeneity, which provided pockets of suitable climate in the southeast, whereas ecosystems in the north and central regions were homogeneous. Generally, our results imply that mountainous regions with high environmental heterogeneity and high genetic diversity may buffer the adverse impacts of climate change on species distribution and intraspecific diversity. Therefore, genetic structure and characteristics of the ecosystem may be crucial for conservation under climate change. [ABSTRACT FROM AUTHOR]

Background: Castor (Ricinus communis L.) seeds contain a large amount of oil that has several biological activities. In the current research, phytogeographic distribution, seed morphological characteristics, molecular genetic diversity and structure, and fatty acid composition were investigated in nine Iranian castor populations. Methods and results: The cetyltrimethylammonium bromide (CTAB) protocol was used to extract the nuclear genomes. These were later amplified using 13 SCoT molecular primers. The phytogeographic distribution was determined based on the Zohary mapping, GC apparatus determined the fatty acid composition of the seeds. GenAlex, STRUCTURE, GenoDive, PopGene, and PopART software were used for the statistical analyzes. On phytogeographic mapping, the harvested populations belonged to different districts of the Euro-Siberian and Irano-Turanian regions (Holarctic kingdom). Most of the quantitative morphological traits of the seeds differed significantly (P ≤ 0.05) between the populations. The AMOVA test demonstrated a large proportion of significant genetic diversity assigned among populations, which were approved by some estimated parameters of genetic diversity such as Nm, Ht, Hs, and Gst. Nei's genetic distance and structure analysis confirmed the existence of two main genotype groups and some intermediates. However, there was no isolation by distance between the genotypes. Unsaturated fatty acids were detected as the main component of seed oil with linoleic and ricinoleic acids. Significant correlations were detected between the main fatty acids of seed oil with seed morphological traits, geographic distance and the geographic parameters of habitats. According to the composition of the seed fatty acids, four chemotypes groups were detected. Conclusions: The classification patterns of the populations based on molecular genetic data, fatty acid composition, and phytogeographic mapping were not identical. These findings indicated that Iranian castor populations had unusual seed fatty acid composition which strongly depended on habitat geographic factors and seed morphological traits. However, the identified chemotypes and genotypes can be used in future breeding programs. [ABSTRACT FROM AUTHOR]

The extent and ecological significance of intraspecific functional diversity within marine microbial populations is still poorly understood, and it remains unclear if such strain-level microdiversity will affect fitness and persistence in a rapidly changing ocean environment. In this study, we cultured 11 sympatric strains of the ubiquitous marine picocyanobacterium Synechococcus isolated from a Narragansett Bay (RI) phytoplankton community thermal selection experiment. Thermal performance curves revealed selection at cool and warm temperatures had subdivided the initial population into thermotypes with pronounced differences in maximum growth temperatures. Curiously, the genomes of all 11 isolates were almost identical (average nucleotide identities of >99.99%, with >99% of the genome aligning) and no differences in gene content or single nucleotide variants were associated with either cool or warm temperature phenotypes. Despite a very high level of genomic similarity, sequenced epigenomes for two strains showed differences in methylation on genes associated with photosynthesis. These corresponded to measured differences in photophysiology, suggesting a potential pathway for future mechanistic research into thermal microdiversity. Our study demonstrates that present-day marine microbial populations can harbor cryptic but environmentally relevant thermotypes which may increase their resilience to future rising temperatures. [ABSTRACT FROM AUTHOR]

Abstract Lindera obtusiloba Blume is the northernmost tree species in the family Lauraceae, and it is a key species in understanding the evolutionary history of this family. The species of L. obtusiloba in East Asia has diverged into the Northern and Southern populations, which are geographically separated by an arid belt. Though the morphological differences between populations have been observed and well documented, intraspecific variations at the plastomic level have not been systematically investigated to date. Here, ten chloroplast genomes of L. obtusiloba individuals were sequenced and analyzed along with three publicly available plastomes. Comparative plastomic analysis suggests that both the Northern and the Southern populations share similar overall structure, gene order, and GC content in their plastomes although the size of the plasome and the level of intraspecific variability do vary between the two populations. The Northern have relatively larger plastomes while the Southern population possesses higher intraspecific variability, which could be attributed to the complexity of the geological environments in the South. Phylogenomic analyses also support the split of the Northern and Southern clades among L. obtusiloba individuals. However, there is no obvious species boundary between var. obtusiloba and var. heterophylla in the Southern population, indicating that gene flow could still occur between these two varieties, and this could be used as a good example of reticulate evolution. It is also found that a few photosynthesis‐related genes are under positive selection, which is mainly related to the geological and environmental differences between the Northern and the Southern regions. Our results provide a reference for phylogenetic analysis within species and suggest that phylogenomic analyses with a sufficient number of nuclear and chloroplast genomic target loci from widely distributed individuals could provide a deeper understanding of the population evolution of the widespread species.

Abstract Gnathopogon caerulescens, an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stressed on the importance of incorporating genetic diversity for conservation purposes. In this study, we aimed to evaluate the mitochondrial DNA haplotype composition of G. caerulescens using environmental DNA (eDNA) to determine the genetic diversity of this species. We developed an eDNA‐based haplotyping approach using high‐throughput sequencing (HTS), which can accurately detect and eliminate erroneous HTS reads, even when the target sequences are differentiated by a single or a few mismatches. Field surveys using the developed method successfully revealed the genetic structure of local G. caerulescens populations. We found star‐shaped haplotype networks with two major haplotypes accompanied by several rare haplotypes for all local populations except one, which suggested that the G. caerulescens population had undergone a historical expansion, and its population size did not shrink to the extent that rare haplotypes were eliminated during the population decline in the 1990s. We also observed that the genetic diversity was lower in the northern populations in terms of haplotype number and haplotype diversity (h), suggesting that the decline in population was more severe in the north than in the south. We demonstrated the practical use of eDNA analysis in population genetics of endangered species. Continuous monitoring using this approach would facilitate the conservation and management of fish resources.

Phaseolus species are cultivated worldwide as a primary food source for human consumption. Common bean (Phaseolus vulgaris L.) and runner bean (Phaseolus coccineus L.) landraces are often cultivated together. The purpose was to document the traditional knowledge held by farmers regarding bean landraces, to describe the diversity through seed morphological descriptors (five quantitative and five qualitative traits), to understand the geographic distribution using Moran’s I statistic, and to analyze the diversity through the Shannon–Wiener Diversity–Equity (H′) index and the Shannon J’ homogeneity index at the community level to better understand the richness of this geographic area. A total of 361 common and runner bean accessions were collected in 10 Andean rural communities of Cotacachi, North Ecuador. We identified 47 landraces, predominantly kept by indigenous female farmers, with limited access to formal education, highlighting the role of this disadvantaged population in agrobiodiversity conservation. The cluster analysis revealed three groups (cophenetic correlation coefficient = 0.6). In the principal component (PC) analysis, 94% of the variation was explained by PC1 and PC2. A positive spatial autocorrelation (Moran’s I: 0.24; z-score: 2.20; p-value: 0.03) was identified, confirming a spatial structure. The Morochos community showed the highest diversity (H′ = 1.55). The information of the diversity and distribution of common and runner bean variability provided in this study is a contribution to further research focused on conservation.

Abstract Following the EFSA commodity risk assessment of Malus domestica plants imported from Türkiye into the EU, the EFSA Panel on Plant Health performed a pest categorisation of Pratylenchus loosi (Nematoda: Pratylenchidae) for the EU. Pratylenchus loosi belongs to the order Rhabditida, subfamily Pratylenchidae. This nematode is not known to be present in the EU. The species is not included in the EU Commission Implementing Regulation 2019/2072. The pest occurs primarily in tropical, subtropical and warm temperate areas. It is widely distributed in Asian countries, with tea plants (Camellia sinensis) as the main host. The pest was reported from more than 60 plant species, but reports from hosts other than C. sinensis, e.g. citrus (Citrus spp.) and banana (Musa spp.), are associated with high uncertainty due to doubtful pest identification. Morphological and molecular methods are available for the identification of the pest. Pathways of entry are host plants for planting except seeds, as well as soil attached to plants for planting, machinery or footwear. Soil import to the EU is prohibited from third countries. The climatic preferences of P. loosi are compatible with the microclimatic conditions occurring in the areas of the EU where tea is grown outside. The impact of the nematode is primarily known for Asian countries, where it is a devastating pathogen on tea plants, but there is a key uncertainty on impacts on hosts other than tea. Considering the strong pathogenicity of the pest, its establishment in tea producing areas would have negative consequences for tea producers. Therefore, the Panel concludes that P. loosi satisfies all the criteria that are within the remit of EFSA to assess for it to be regarded as a potential Union quarantine pest.

Abstract Plant–herbivore interactions mediated by plant–plant signalling have been documented in different species but its within‐species variability has hardly been quantified. Here, we tested if herbivore foraging activity on plants was influenced by a prior contact with a damaged plant and if the effect of such plant–plant signalling was variable across 113 natural genotypes of Arabidopsis thaliana. We filmed the activity of the generalist herbivore Cornu aspersum during 1 h on two plants differing only in a prior contact with a damaged plant or not. We recorded each snails' first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption. Overall, plant–plant signalling modified the foraging activity of herbivores in A. thaliana. On average, snails spent more time and consumed more of plants that experienced a prior contact with a damaged plant. However, the effects of plant–plant signalling on snail behaviour was variable: depending on genotype identity, plant–plant signalling made undamaged plants more repellant or attractive to snails. Genome‐wide associations revealed that genes related to stress coping ability and jasmonate pathway were associated to this variation. Together, our findings highlight the adaptive significance of plant–plant signalling for plant–herbivore interactions.

Climate change is altering the multifunctionality of ecosystems worldwide and is often associated with changes in biodiversity that can modulate the impacts of climate change on ecosystems through interactive effects. Genetic and phenotypic variation within species are particularly influenced by climatic conditions, and can mediate several ecosystem processes. Here, we tested whether temperature can interact with intraspecific variation to drive ecosystem multifunctionality. Using a common gardening experiment, we test the consequences of intraspecific variation (population identity and trait variation) of a consumer fish species (European minnow Phoxinus phoxinus) and temperature on ecosystem multifunctionality, as well as on the biomass of a subsequent fish generation (long‐term effects). We found that individuals from different populations affect ecosystem multifunctionality independently of temperature, and that multifunctionality differed between cold and warm mesocosms. Moreover, when investigating sub‐components of multifunctionality, we found a positive relationship between individual metabolic rate and multifunctional primary production in warm mesocosms, whereas this relationship was reversed in cold mesocosms. We similarly found evidence that the long‐term effect of intraspecific trait variation on the biomass of the next fish generation was temperature‐dependent. These findings demonstrate that differences among populations can have strong consequences on ecosystem multifunctionality, and that intraspecific variation must be considered in addition to other components of global change to predict the impacts of global change on ecosystem multifunctionality. [ABSTRACT FROM AUTHOR]

Individual‐level trait diversity has been identified as an essential component of trait diversity (TD), influencing community assembly and structure. Traditionally, one employs trait diversity indices to measure facets of individual‐level trait diversity (divergence, richness and evenness). However, the application of species‐level trait diversity indices to individual‐level traits data and their implications have not been adequately studied. Thus, we examined the possible challenges of using four commonly used multi‐trait TD indices: Rao's quadratic entropy (Rao), functional dispersion (FDis), functional evenness (FEve) and functional richness (FRic); two indices primarily developed to measure individual‐level trait diversity: trait evenness distribution (TED‐for evenness) and trait onion peeling (TOP‐for richnness); and a modified version of TED (TEDM‐for evenness). Additionally, we considered an index that integrates both evenness and richness by generalizing ordinary Hill indices for traits (coined HIT). We measured individual‐level trait diversity with these indices using simulated traits data and experimental data from a growth experiment with cyanobacteria. Comparing the observed trends from the indices with the expected trends, we observed that only the trait divergence indices (FDis and Rao) produced the expected trends in the simulation scenarios and experimental data. TED and TEDM are not robust against the number of individuals used, and FEve is not sensitive to some changes in the location of individuals in the trait space. Also, TOP proved to be a discontinuous function dependent on the number of individuals, and FRic did not produce the anticipated trend when changes in the trait space did not affect the edges of the trait space. HIT did produce the anticipated changes, but it was only reliable when many individuals were sampled. In summary, applying these individual‐level trait diversity indices to quantify anything except trait divergence may lead to misinterpretation of the original situation of trait distribution in the trait space if their specific properties are not adequately considered. [ABSTRACT FROM AUTHOR]

Plant–herbivore interactions mediated by plant–plant signalling have been documented in different species but its within‐species variability has hardly been quantified. Here, we tested if herbivore foraging activity on plants was influenced by a prior contact with a damaged plant and if the effect of such plant–plant signalling was variable across 113 natural genotypes of Arabidopsis thaliana. We filmed the activity of the generalist herbivore Cornu aspersum during 1 h on two plants differing only in a prior contact with a damaged plant or not. We recorded each snails' first choice, and measured its first duration on a plant, the proportion of time spent on both plants and leaf consumption. Overall, plant–plant signalling modified the foraging activity of herbivores in A. thaliana. On average, snails spent more time and consumed more of plants that experienced a prior contact with a damaged plant. However, the effects of plant–plant signalling on snail behaviour was variable: depending on genotype identity, plant–plant signalling made undamaged plants more repellant or attractive to snails. Genome‐wide associations revealed that genes related to stress coping ability and jasmonate pathway were associated to this variation. Together, our findings highlight the adaptive significance of plant–plant signalling for plant–herbivore interactions. [ABSTRACT FROM AUTHOR]

The phylogeographic structure of the endemic white-toothed shrews of Vietnam, which belong to the Crocidura kegoensis–C. zaitsevi group, was assessed using mitochondrial and nuclear data. Specimens from 12 localities across Vietnam, including the holotypes of C. kegoensis and C. zaitsevi, were evaluated according to the complete mitochondrial cytochrome b (cytb) gene and fragments of eight independent nuclear loci. The results of molecular analyses revealed the conspecificity of C. kegoensis and C. zaitsevi. Therefore, the name Crocidura zaitsevi Jenkins et al., 2007, can be considered as a synonym of C. kegoensis Lunde et al., 2004, which has a complex phylogeographical structure. The analysis of cytb proved the existence of distinct mtDNA lineages in C. kegoensis: lineage A, which is distributed in the northern and central parts of the Annamite Range; and lineage B, which is only found in the south parts of the species range. Nuclear data support the differentiation between northern and southern populations, with the position of the central populations remaining unresolved. The estimated divergence times of the main mitochondrial lineages indicate that the Vietnamese endemic group, C. kegoensis−C. zaitsevi, represents a young taxon, with all radiation events occurring in the cooling periods of the Pleistocene. [ABSTRACT FROM AUTHOR]

Throughout their life cycle, plants are subjected to a variety of environmental constraints, including abiotic stresses. The present study aimed at characterizing the responses of the two tomato cultivars Gold Nugget (GN) and Purple Calabash (PC) exposed to a combination of nickel (Ni) and drought. The following hypotheses were pursued: (i) the activation of responses to one stressor eases further adjustments to a second stressor; and (ii) the two tomato cultivars are differentially susceptible to drought and heavy metal-stress. Besides biometrical evaluations, the distribution of Ni in tissues and the redox homeostasis in both cultivars were compared in response to Ni-stress, polyethylene glycol (PEG)-induced drought, and to their combination. Regarding single stresses, Ni caused more harmful effects to plants than PEG-induced drought, in terms of growth inhibition and production of reactive oxygen species. Ni was mostly accumulated in the roots. The GN cultivar promptly activated antioxidant defenses under Ni-stress, while, in PC, such antioxidants were more strongly induced under combined stress. Stress co-exposure led to a drastic proline accumulation, resembling a signal of stress sensitivity. Overall, the GN cultivar seemed to be less susceptible to the combined stress than PC, as it could activate stronger antioxidant defenses under single Ni toxicity, possibly easing further adjustments demanded by the later co-exposure to drought. This study showed that the two cultivars of the same species had different levels of perception and responsiveness to Ni-induced stress, which translated into different susceptibilities to the combined exposure to PEG-induced drought. [ABSTRACT FROM AUTHOR]

Habitat restoration is an important tool used to conserve biodiversity and restore species, but its effects are notoriously difficult to predict. Although outcomes of restoration projects are usually assessed using indices of species abundance and diversity, phenotypic differences among individuals within species are likely associated with differing responses to restored habitats. Here, we use lake sturgeon (Acipenser fulvescens) as a case study to illustrate how responses to habitat restoration can differ between phenotypes and potentially lead to unanticipated effects on populations. North America’s St. Clair River supports one of the largest remaining populations of lake sturgeon but has lost much spawning habitat due to its role as a major industrial corridor between the Laurentian Great Lakes Erie and Huron. Two artificial reefs were recently built in the lower and middle segments of the river to increase the available sturgeon spawning habitat. Interestingly, lake sturgeon in the St. Clair River express different migratory phenotypes that may be associated with different likelihoods of colonizing artificial reefs. Acoustic telemetry revealed that artificial reefs were more likely to be used by sturgeon that migrated downstream to overwinter in Lake St. Clair than those that migrated upstream to overwinter in Lake Huron. Furthermore, increasing time spent at the artificial reefs by Lake St. Clair migrants was associated with later arrival to and shorter occupancy of the river’s only natural spawning site, the primary location where the two phenotypes have opportunity to interbreed. Additional research is necessary to determine the ultimate impacts of the artificial reefs on lake sturgeon populations; nevertheless, our study showed phenotype-specific opportunity to colonize restored habitat and a mechanism through which this could lead to changes in gene flow. Our results illustrate the importance of considering intra-specific diversity when planning restoration projects and assessing the effects on populations.

Lathyrus is the largest genus in the economically important tribe Fabeae. It is used for many purposes in animal feed, planting in low-yield lands, cold resistance, water shortage, and increasing soil fertility. To evaluate the yield and morphological traits of 44 accessions of six species of the genus Lathyrus including one accession of L. aphaca var. aphaca, seven accessions of L. cassius, one accession of L. chloranthus, two accessions of L. cicera, 22 accessions of L. inconspicuus and nine accessions of L. sativus, were studied as a randomized complete block design with three replications at Alborz Research Station in Karaj. The results showed that there was a significant difference between L. cassius and L. inconspicuus accessions in morphological characteristics except for flowering time and seed maturity. The studied populations of L. sativus in addition to flowering time and seed maturity did not show diversity in plant dry weight, biomass production, and pod characteristics. The field potential of 44 accessions of the six studied species with different geographical origins under constant field conditions showed no relationship with their geographical origin. Thus, it can be stated that the similarity between the accessions is not due to their geographical origin, and the natural distribution of Lathyrus species has been separated by crop cultivars. However, the observed diversity suggests that genetic improvement is potentially possible through crossbreeding and selection. Then the simultaneous appearance of two traits of high biomass yield and taller plant height in an accession was recognized as a distinguishing feature, and accessions with the above characteristics can be used as parents. [ABSTRACT FROM AUTHOR]

Atriplex canescens is a polymorphic species that can be deciduous or evergreen depending on the climate. Having an extensive root system, it controls soil erosion very well and is resistant to drought. The present study examined the morphological and genetic diversity of 13 Iranian populations. Multivariate statistical analyses were performed on 25 morphological characteristics (quantitative and qualitative). To assess genetic diversity, eight primers were applied, resulting in 42 bands. With the ANOVA test, all quantitative morphological characteristics among the studied populations were significantly different. Similarly, the AMOVA test revealed that the genetic content of the studied populations was different. Genetic distance and geographic distance were significantly correlated in Mantel's test. Based on morphological studies and the effects of environmental factors (latitude, longitude, and altitude) on genetic structure, different genetic branches have been proposed for A. canescens. [ABSTRACT FROM AUTHOR]

(a) An eelgrass meadow in Bodega Harbor, CA seemingly lacks diversity given that only one macrophyte species dominates the seascape, the marine angiosperm Zostera marina. Although the magnitude of eelgrass genotypic richness itself was not surprising (Hughes & Stachowicz, 2009; Kamel et al., 2012; Reynolds et al., 2017), coordinate-based mapping showed that these genotypes are naturally intertwined at the scale of only a few centimeters. Eelgrass genotypes show considerable genetically based phenotypic variation in traits that influence the outcome of intergenotypic interactions (Abbott & Stachowicz, 2016). Keywords: clonality; diversity maintenance; diversity mapping; ecological genetics; intraspecific diversity; seagrass; spatial variation EN clonality diversity maintenance diversity mapping ecological genetics intraspecific diversity seagrass spatial variation 1 5 5 11/03/22 20221101 NES 221101 At first glance, images of homogenous-looking green seagrass meadows (Figure 1a) do not epitomize "biodiversity" in the way that species-rich mosaics of coral reefs or rainforests might. [Extracted from the article]

Despite the potential of standing genetic variation to rescue communities and shape future adaptation to climate change, high levels of uncertainty are associated with intraspecific trait variation in marine phytoplankton. Recent model intercomparisons have pointed to an urgent need to reduce uncertainty in the projected responses of marine ecosystems to climate change, including Southern Ocean (SO) surface waters, which are among the most rapidly warming habitats on Earth. Because SO phytoplankton growth responses to warming sea surface temperature (SST) are poorly constrained, we developed a high‐throughput growth assay to simultaneously examine inter‐ and intra‐specific thermal trait variation in a group of 43 taxonomically diverse and biogeochemically important SO phytoplankton called diatoms. We found significant differential growth performance among species across thermal traits, including optimum and maximum tolerated growth temperatures. Within species, coefficients of variation ranged from 3% to 48% among strains for those same key thermal traits. Using SO SST projections for 2100, we predicted biogeographic ranges that differed by up to 97% between the least and most tolerant strains for each species, illustrating the role that strain‐specific differences in temperature response can play in shaping predictions of future phytoplankton biogeography. Our findings revealed the presence and scale of thermal trait variation in SO phytoplankton and suggest these communities may already harbour the thermal trait diversity required to withstand projected 21st‐century SST change in the SO even under severe climate forcing scenarios. [ABSTRACT FROM AUTHOR]

The pollution of freshwater ecosystems is threatening freshwater plant species diversity worldwide. Freshwater plants, such as the common duckweed (Lemna minor), are potentially sensitive to novel stressful environments. To test if ecotype diversity could increase resistance to stressful environments, I used seven L. minor populations and measured their growth rates with and without moderate salt stress across an ecotype diversity gradient. The L. minor populations were grown over 5 months in 92 experimental mesocosms, either in ecotype monocultures or in polyculture with either one or three conspecific ecotypes (23 unique compositions). After growing the duckweed in unperturbed conditions (phase 1), the cultures were subjected to moderate salt stress (50 mmol/L NaCl) for several weeks (phase 2). The experiment was conducted in the presence of the natural epimicrobial community associated with the different ecotypes. In phase 2, a subset of these algae added an unintentional second stressor to the experiment. The ecotypes differed in their growth rates, the fastest growing at twice the rate of others. The diversity context further shaped the ecotype growth rates. Ecotype polycultures showed higher abundances towards the end of the experiment, thus over time, as the environment deteriorated, ecotype diversity gained in importance. These findings show that within-species variation in growth rates can translate to a positive effect of ecotype diversity on population abundance. Exposure of L. minor to moderate salt levels did not significantly impact growth rates, although the effect may have been masked by reduced algal stress in the saline environments. [ABSTRACT FROM AUTHOR]

Two bacterial strains, KH365_2T and KH569_7, were isolated from the cecum contents of wild-derived house mice. The strains were characterized as Gram-negative, rod-shaped, strictly anaerobic, and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences revealed that both strains were most closely related to Bacteroides uniformis ATCC 8492T. Whole genome sequences of KH365_2T and KH569_7 strains have a DNA G + C content of 46.02% and 46.03% mol, respectively. Most morphological and biochemical characteristics did not differ between the newly isolated strains and classified Bacteroides strains. However, the average nucleotide identity (ANI) and dDNA–DNA hybridization (dDDH) values clearly distinguished the two strains from described members of the genus Bacteroides. Here, we present the phylogeny, morphology, and physiology of a novel species of the genus Bacteroides and propose the name Bacteroides muris sp. nov., with KH365_2T (DSM 114231T = CCUG 76277T) as type strain. [ABSTRACT FROM AUTHOR]

Intraspecific genetic diversity is heterogeneously distributed in natural landscapes and often forms repeatable spatial patterns. For instance, in rivers, genetic diversity increases towards downstream areas, whereas genetic differentiation increases in isolated upstream areas. Nonetheless, these patterns can be modified by human‐induced perturbations, and documenting the extent to which human activities alter these natural patterns is important for conservation. Among the human pressures that affect freshwater biodiversity, stocking natural populations with captive‐bred strains is a common practice worldwide that can strongly alter the genetic integrity of wild populations.The main objectives of this study were to document the spatial distribution of captive‐bred ancestry in brown trout (Salmo trutta) populations from four French basins having been stocked according to different practices, and to quantify for each basin the effect of captive‐bred ancestry on the spatial distribution of genetic diversity and differentiation. The four basins were sampled along their upstream–downstream gradient, and a total of 1,686 individuals were genotyped at 192 single nucleotide polymorphism loci.For all basins, individuals with a strong assignment to the captive strain were mostly found in upper reaches, although the average proportion of captive‐bred ancestry varied strikingly among rivers (from 1.9 to 58.7%). Although spatial patterns of genetic differentiation were not affected by introgression and showed an expected increase with increasing distances from the river mouth in all basins, there was evidence that the classical pattern of downstream increase in genetic diversity was reversed when considering highly introgressed populations.These findings demonstrate that the stocking of captive‐bred strains can strongly modify natural spatial patterns of diversity, even when stocking occurred many generations ago and has now ended. The study illustrates the major impacts of humans on intraspecific biodiversity patterns, and emphasizes the importance of conservation plans that take into account this artificial distribution of genetic diversity. [ABSTRACT FROM AUTHOR]

Intraspecific variation in specialized metabolites plays a crucial role in the adaptive response to diverse environments. Two major subspecies, japonica and indica, are observed in Asian cultivated rice (Oryza sativa L.). Previously, we identified (3R)-β-tyrosine, a novel nonproteinogenic β-amino acid in plants, along with the enzyme tyrosine aminomutase (TAM1), which is required for β-tyrosine biosynthesis, in the japonica cultivar Nipponbare. Notably, TAM1 and β-tyrosine were preferentially distributed in japonica cultivars compared with indica cultivars. Considering its phytotoxicity and antimicrobial activity, intraspecific variation in β-tyrosine may contribute to the defensive potential of japonica rice. Investigation of the evolutionary trajectory of TAM1 and β-tyrosine should enhance our understanding of the evolution of rice defense. However, their distribution patterns in O. rufipogon, the direct ancestor of O. sativa, remain unclear. Therefore, in this study, we extensively examined TAM1 presence/absence and β-tyrosine content in 110 genetically and geographically diverse O. rufipogon accessions and revealed that they are characteristically observed in the ancestral subpopulation of japonica rice, while being absent or slightly accumulated in other subpopulations. Thus, we conclude that TAM1 and β-tyrosine in japonica rice are likely derived from its ancestral subpopulation. Furthermore, the high and low TAM1 possession rates and β-tyrosine content in japonica and indica rice, respectively, could be attributed to distribution patterns of TAM1 and β-tyrosine in their ancestral subpopulations. This study provides fundamental insights into the evolution of rice defense.

Turfgrass lawns are synonymous with plant selection in the built environment. Plants in urban landscapes are largely selected to enhance aesthetic quality and comply with social norms. Warm season turfgrasses are produced and planted as intraspecific cultivar monocultures to preserve heritable traits that meet aesthetic standards. Monocultures are less resilient to biotic and abiotic stress than more diverse plantings, which increases reliance on pesticides and resource-intensive maintenance and presents unintended environmental risks. Increasing interspecific plant diversity may provide the greatest resilience benefits, but it introduces production, maintenance, and marketing barriers that can inhibit industry and consumer acceptance. Intraspecific cultivar blends may provide plant diversity resilience benefits without compromising industry and consumer values. Using a four-year field experiment we determined the effects of mixing warm season turfgrass cultivars on lawn resilience and aesthetic quality. We find that mixing turfgrass cultivars increases quality compared to cultivar monocultures, but primarily when a poorly performing cultivar is present. Mixtures of four cultivars containing the poorly performing cultivar averaged 42% greater plant cover and 33% greater aesthetic quality than monocultures of that cultivar, indicating that the other cultivars compensated for the loss of one from the stand. Three years after planting, perceived aesthetic quality of lawns by turfgrass industry professionals was above the minimum aesthetic threshold only for plots containing blends of four cultivars. Thus, our results suggest that mixing warm season turfgrass cultivars extends the longevity of turfgrass coverage and quality compared to conventional cultivar monocultures. Such benefits can reduce monetary, natural resource, and pesticide inputs without conflicting with social aesthetic norms and may be a ready-made approach to more sustainable lawns in urban greenspaces. [ABSTRACT FROM AUTHOR]

Lack of research on intraspecific diversity of faba bean and its management in Ethiopia could lead to the loss of farmers' varieties, limiting the contributions of local genetic resources. This study assessed the diversity of farmers' faba bean varieties and local knowledge related to their use and management across multiple cultural and agroecological contexts. We conducted 288 structured and 48 semi-structured interviews in five agroecological zones and four cultural areas in northeastern and southwestern Ethiopia. A total of seventeen farmers' varieties were identified and documented based on phenotypic descriptors. The tepid sub-moist mid-highlands of South Wollo had the highest number of varieties (five) of any area sampled; however, the humid mid-highlands of Jimma had a higher Shannon-Wiener diversity index based on the area planted to each variety. Most farmers reported that they had originally obtained their traditional varieties from family members, whereas new varieties were typically purchased from local markets. According to farmers, both male and female adults participated in the production and processing of faba bean, with some distinct differences among cultural areas. Understanding the diversity of farmers' varieties has important implications for on-farm conservation strategies to enhance the use value of this multipurpose leguminous crop. [ABSTRACT FROM AUTHOR]

Samples of two duckweed species, Spirodela polyrhiza and Lemna minor, were collected around small ponds and investigated concerning the question of whether natural populations of duckweeds constitute a single clone, or whether clonal diversity exists. Amplified fragment length polymorphism was used as a molecular method to distinguish clones of the same species. Possible intraspecific diversity was evaluated by average-linkage clustering. The main criterion to distinguish one clone from another was the 95% significance level of the Jaccard dissimilarity index for replicated samples. Within natural populations of L. minor, significant intraspecific genetic differences were detected. In each of the three small ponds harbouring populations of L. minor, based on twelve samples, between four and nine distinct clones were detected. Natural populations of L. minor consist of a mixture of several clones representing intraspecific biodiversity in an aquatic ecosystem. Moreover, identical distinct clones were discovered in more than one pond, located at a distance of 1 km and 2.4 km from each other. Evidently, fronds of L. minor were transported between these different ponds. The genetic differences for S. polyrhiza, however, were below the error-threshold of the method within a pond to detect distinct clones, but were pronounced between samples of two different ponds. [ABSTRACT FROM AUTHOR]

Climate‐modulated parasitism is driven by a range of factors, yet the spatial and temporal variability of this relationship has received scant attention in wild vertebrate hosts. Moreover, most prior studies overlooked the intraspecific differences across host morphotypes, which impedes a full understanding of the climate–parasitism relationship. In the common lizard (Zootoca vivipara), females exhibit three colour morphs: yellow (Y‐females), orange (O‐females) and mixed (mixture of yellow and orange, M‐females). Zootoca vivipara is also infested with an ectoparasite (Ophionyssus mites). We therefore used this model system to examine the intraspecific response of hosts to parasitism under climate change. We found infestation probability to differ across colour morphs at both spatial (10 sites) and temporal (20 years) scales: M‐females had lower parasite infestations than Y‐ and O‐females at lower temperatures, but became more susceptible to parasites as temperature increased. The advantage of M‐females at low temperatures was counterbalanced by their higher mortality rates thereafter, which suggests a morph‐dependent trade‐off between resistance to parasites and host survival. Furthermore, significant interactions between colour morphs and temperature indicate that the relationship between parasite infestations and climate warming was contingent on host morphotypes. Parasite infestations increased with temperature for most morphs, but displayed morph‐specific rates. Finally, infested M‐females had higher reductions in survival rates than infested Y‐ or O‐females, which implies a potential loss of intraspecific diversity within populations as parasitism and temperatures rise. Overall, we found parasitism increases with warming temperatures, but this relationship is modulated by host morphotypes and an interaction with temperature. We suggest that epidemiological models incorporate intraspecific diversity within species for better understanding the dynamics of wildlife diseases under climate warming. [ABSTRACT FROM AUTHOR]

Abstract Loss of plant biodiversity can result in reduced abundance and diversity of associated species with implications for ecosystem functioning. In ecosystems low in plant species diversity, such as Neotropical mangrove forests, it is thought that genetic diversity within the dominant plant species could play an important role in shaping associated communities. Here, we used a manipulative field experiment to study the effects of maternal genotypic identity and genetic diversity of the red mangrove Rhizophora mangle on the composition and richness of associated soil bacterial communities. Using terminal restriction fragment length polymorphism (T‐RFLP) community fingerprinting, we found that bacterial community composition differed among R. mangle maternal genotypes but not with genetic diversity. Bacterial taxa richness, total soil nitrogen, and total soil carbon were not significantly affected by maternal genotypic identity or genetic diversity of R. mangle. Our findings show that genotype selection in reforestation projects could influence soil bacterial community composition. Further research is needed to determine what impact these bacterial community differences might have on ecosystem processes, such as carbon and nitrogen cycling.