Variation In Species Research Articles

Canopy-Level Spectral Variation and Classification of Diverse Crop Species with Fine Spatial Resolution Imaging Spectroscopy

Canopy-Level Spectral Variation and Classification of Diverse Crop Species with Fine Spatial Resolution Imaging Spectroscopy

Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park

Utilising public sequence databases to investigate genetic diversity of stoneflies in Medvednica Nature Park

Genomic insights into local adaptation and vulnerability of Quercus longinux to climate change

BackgroundClimate change is expected to alter the factors that drive changes in adaptive variation. This is especially true for species with long life spans and limited dispersal capabilities. Rapid climate changes may disrupt the migration of beneficial genetic variations, making it challenging for them to keep up with changing environments. Understanding adaptive genetic variations in tree species is crucial for conservation and effective forest management. Our study used landscape genomic analyses and phenotypic traits from a thorough sampling across the entire range of Quercus longinux, an oak species native to Taiwan, to investigate the signals of adaptation within this species.ResultsUsing ecological data, phenotypic traits, and 1,933 single-nucleotide polymorphisms (SNPs) from 205 individuals, we classified three genetic groups, which were also phenotypically and ecologically divergent. Thirty-five genes related to drought and freeze resistance displayed signatures of natural selection. The adaptive variation was driven by diverse environmental pressures such as low spring precipitation, low annual temperature, and soil grid sizes. Using linear-regression-based methods, we identified isolation by environment (IBE) as the optimal model for adaptive SNPs. Redundancy analysis (RDA) further revealed a substantial joint influence of demography, geology, and environments, suggesting a covariation between environmental gradients and colonization history. Lastly, we utilized adaptive signals to estimate the genetic offset for each individual under diverse climate change scenarios. The required genetic changes and migration distance are larger in severe climates. Our prediction also reveals potential threats to edge populations in northern and southeastern Taiwan due to escalating temperatures and precipitation reallocation.ConclusionsWe demonstrate the intricate influence of ecological heterogeneity on genetic and phenotypic adaptation of an oak species. The adaptation is also driven by some rarely studied environmental factors, including wind speed and soil features. Furthermore, the genetic offset analysis predicted that the edge populations of Q. longinux in lower elevations might face higher risks of local extinctions under climate change.

In silico search for and analysis of R gene variation in primitive cultivated potato species.

Pathogen recognition receptors encoded by R genes play a key role in plant protection. Nowadays, R genes are a basis for breeding many crops, including potato. Many potato R genes have been discovered and found suitable for breeding thanks to the studies of a wide variety of wild potato species. The use of primitive cultivated potato species (PCPS) as representatives of the primary gene pool can also be promising in this respect. PCPS are the closest to the early domesticated forms of potato; therefore, their investigation could help understand the evolution of R genes. The present study was aimed at identifying and analyzing R genes in PCPS listed in the open database of NCBI and Solomics DB. In total, the study involved 27 accessions belonging to three species: Solanum phureja Juz. & Bukasov, S. stenotomum Juz. & Bukasov and S. goniocalyx Juz. & Bukasov Materials for the analysis were the sequencing data for the said three species from the PRJNA394943 and PRJCA006011 projects. An in silico search was carried out for sequences homologous to 26 R genes identified in potato species differing in phylogenetic distance from PCPS, namely nightshade (S. americanum), North- (S. bulbocastanum, S. demissum) and South-American (S. venturii, S. berthaultii) wild potato species, as well as the cultivated potato species S. tuberosum and S. andigenum. Homologs of all investigated protein-coding sequences were discovered in PCPS with a relatively high degree of similarity (85-100 %). Homologs of the Rpi-R3b, Rpi-amr3 and Rpi-ber1 genes have been identified in PCPS for the first time. An analysis of polymorphism of nucleotide and amino acid sequences has been carried out for 15 R genes. The differences in frequencies of substitutions in PCPS have been demonstrated by analysis of R genes, the reference sequences of which have been identified in different species. For all the studied NBS-LRR genes, the proportion of substituted amino acids in the LRR domain exceeds this figure for the NBS domain. The potential prospects of using PCPS as sources of resistance to Verticillium wilt have been shown.

Cranial variation in species and subspecies of kangaroo rats (Dipodomys, Dipodomyinae, Rodentia) according to geometric morphometrics.

Traditional Dipodomys (sub)species identification uses geography, phenotype, and external/skull measurements. Such measurements are correlated with size and thus redundant. I assessed the value of scaled cranial shape, based on two-dimensional landmarks (analyzed using geometric morphometric methods) in distinguishing Dipodomys taxa, and in summarizing their variation. My dataset includes 601 adult specimens from 20 species (49 operational taxonomic units - OTUs) across 190 localities. Cranial shape was highly useful in classifying Dipodomys taxa without considering geography. The auditory bulla was the most variable region-taxa differed in its hypertrophy, accompanied by different degrees of nearby structure crowding. Cranial shape was weakly allometric, with no significant sexual dimorphism. Weak size dimorphism was detected. (Sub)specific taxonomy is not reflective of shape variation, as the number of subspecies per species is not associated with disparity. Shape had significant phylogenetic signal, but subspecies did not always cluster with conspecifics and species did not always cluster according to phylogenetic relationship/taxonomy. Shape variation was correlated with climate, and species differed in morphological disparity and degree of specialization, which may contribute to divergence in shape variation patterns from phylogeny. D. deserti was the most specialized species, diverging greatly from the genus mean; D. heermanni was the least specialized. This study provides new insights into morphological variation of North American keystone species, several of conservation interest, for example, D. heermanni berkeleyensis, D. h. dixoni, D. nitratoides brevinasus, and D. n. nitratoides.

Mitochondrial genome variation and intergenomic sequence transfers in Hevea species.

Among the Hevea species, rubber tree (Hevea brasiliensis) is the most important source of natural rubber. In previous studies, we sequenced the complete nuclear and chloroplast genomes of Hevea species, providing an invaluable resource for studying their phylogeny, disease resistance, and breeding. However, given that plant mitochondrial genomes are more complex and more difficult to assemble than that of the other organelles, little is known about their mitochondrial genome, which limits the comprehensive understanding of Hevea genomic evolution. In this study, we sequenced and assembled the mitochondrial genomes of four Hevea species. The four mitochondrial genomes had consistent GC contents, codon usages and AT skews. However, there were significant differences in the genome lengths and sequence repeats. Specifically, the circular mitochondrial genomes of the four Hevea species ranged from 935,732 to 1,402,206 bp, with 34-35 unique protein-coding genes, 35-38 tRNA genes, and 6-13 rRNA genes. In addition, there were 17,294-46,552 bp intergenomic transfer fragments between the chloroplast and mitochondrial genomes, consisting of eight intact genes (psaA, rrn16S, tRNA-Val, rrn5S, rrn4.5S, tRNA-Arg, tRNA-Asp, and tRNA-Asn), intergenic spacer regions and partial gene sequences. The evolutionary position of Hevea species, crucial for understanding its adaptive strategies and relation to other species, was verified by phylogenetic analysis based on the protein-coding genes in the mitochondrial genomes of 21 Malpighiales species. The findings from this study not only provide valuable insights into the structure and evolution of the Hevea mitochondrial genome but also lay the foundation for further molecular, evolutionary studies, and genomic breeding studies on rubber tree and other Hevea species, thereby potentially informing conservation and utilization strategies.

The expression of empathy in human's closest relatives, bonobos and chimpanzees: current and future directions.

Empathy is a complex, multi-dimensional capacity that facilitates the sharing and understanding of others' emotions. As our closest living relatives, bonobos (Pan paniscus) and chimpanzees (P. troglodytes) provide an opportunity to explore the origins of hominin social cognition, including empathy. Despite certain assumptions that bonobos and chimpanzees may differ empathically, these species appear to overlap considerably in certain socio-emotional responses related to empathy. However, few studies have systematically tested for species variation in Pan empathic or socio-emotional tendencies. To address this, we synthesise the growing literature on Pan empathy to inform our understanding of the selection pressures that may underlie the evolution of hominin empathy, and its expression in our last common ancestor. As bonobos and chimpanzees show overlaps in their expression of complex socio-emotional phenomena such as empathy, we propose that group comparisons may be as or more meaningful than species comparisons when it comes to understanding the evolutionary pressures for such behaviour. Furthermore, key differences, such as how humans and Pan communicate, appear to distinguish how we experience empathy compared to our closest living relatives.

Effect of commercial probiotics and antibiotics on the growth of Campylobacter isolated from chicken meat in Ho Chi Minh city markets

This study explores the antibiotic susceptibility of Campylobacter, a prominent foodborne pathogen, isolated in Ho Chi Minh city markets and the efficacy of commercial probiotics in inhibiting these bacteria for enhancing food safety and treating Campylobacter infections. Bacteria were isolated from chicken meat in modified coal deoxycholate cefoperazone agar (mCCD), followed by characterization as per standard procedures. Ten isolates with Gram negative, catalase positive and oxidase positive characteristics were collected. Antibiotic susceptibility is ascertained through the determination of the inhibited zone and minimum inhibitory concentration (MIC) of five distinct antibiotics against Campylobacter on Muller Hinton agar plates, culminating in a comprehensive assessment after a 24-hour incubation duration. The antibiotic susceptibility results underscore substantial diversity in Campylobacter isolates among meat samples, thereby accentuating discernible distinctions among the various antibiotic products. The research also evaluated the suitability of 5 commercial probiotic products (re-named as A, B, C, D, and E for fair assessment) by examining their impact on the growth of Campylobacter colonies. The antimicrobial effect of probiotics against Campylobacter is assessed using the agar well diffusion assay and co-culture method. We obtained consistent results from two methods, indicating no variation in Campylobacter species among meat samples but significant variations among probiotic products. The outcomes of this research provide valuable insights into the antimicrobial potential of each probiotic and antibiotic on Campylobacter, informing recommendations for food hygiene practices and underscoring the role of both probiotics and antibiotics in combating Campylobacter infections.

Fifty shades of white: morphological and molecular diversity of the Cadlina laevis species complex (Gastropoda: Nudibranchia) in the North-West Pacific

We provide a morphological examination and a barcoding study to investigate the species identity and variation limits within the Cadlina laevis species complex. Our molecular analysis based on the COI marker revealed seven new clades in the North-West Pacific Cadlina diversity. The distances between these clades are low in some cases (2.08-7.51% overall), and the species delimitation tests gave controversial results (1, 2, 13, 14 groups, depending on the analysis method). This does not allow to conclusively classify this diversity as interspecific or intraspecific. Morphological analysis showed a significant similarity of all examined groups, with minor differences found in the morphology of the central tooth of the radula and the reproductive system. However, these variations fit into the morphological variability of the North Atlantic species Cadlina laevis s.str. and cannot serve as evidence of the isolation of these identified groups. The discovered diversity may represent both a complex of at least 11 very close and cryptic species with not well-established species boundaries, or be a part of a single amphiboreal species Cadlina laevis s.l. This indicates an extremely complex evolutionary history of Cadlina laevis species complex, making this group is an interesting model object for studying speciation in boreal and Arctic communities.

Breeding biology of the Ochre-breasted pipit (Anthus nattereri), with notes on its conservation in the Upper Rio Grande Grasslands, south-eastern Brazil

ABSTRACT The Ochre-breasted pipit Anthus nattereri is a terrestrial bird restricted to natural grasslands of south-eastern South America. The species is globally Vulnerable to extinction and its natural history is still poorly known. We investigated the breeding biology of Ochre-breasted pipits, commenting on its habitat use and the potential impacts of local grasslands management practices with fire on the species’ conservation. Fieldwork took place mainly between January and December 2016 in the Upper Rio Grande Grasslands, south-eastern Brazil. Five nests of the species were found between September and November, one of them recently destroyed by fire. Nests were cup shaped and placed on the ground, being built with dry grasses, resembling the pattern documented for other species of Anthus. The eggs were covered with brownish spots and dots to a variable extent and the background colour ranged from greyish white to brownish white. The egg colour pattern also fell within the known range of variation for congeneric species, as did the clutch size (two to three eggs) observed in tropical species of Anthus. Ochre-breasted pipits tended to occupy nesting sites with higher and denser grass cover (eg small patches of vegetation that survived the last fire event) when compared to non-nest sites located in adjacent recently burned areas, which potentially suggests a preference for such habitat attributes. Although the Ochre-breasted pipit is relatively common in the study area, the highest temporal incidence of fire coincides with its breeding season, which can directly impact the local population through the burning of nests and the elimination of suitable nesting sites. Thus, it is important to conduct long-term studies to evaluate the impact of different fire regimes on the reproductive performance of Ochre-breasted pipits, thus allowing the design of better ecosystem management practices to guarantee its conservation.

Intra and interspecific variation in thermal performance and critical limits in anurans from southern Chile

The relationship between temperature and performance can be illustrated through a thermal performance curve (TPC), which has proven useful in describing various aspects of ectotherms' thermal ecology and evolution. The parameters of the TPC can vary geographically due to large-scale variations in environmental conditions. However, only some studies have attempted to quantify how thermal performance varies over relatively small spatial scales, even in the same location or consistently among individuals within a species. Here, we quantified individual and species variation in thermal sensitivity of locomotor performance in five amphibia Eupsophus species found in the temperate rainforests of southern Chile and compared their estimates against co-occurring species that exhibit a substantially more extensive distributional range. We measured critical thermal limits and jumping performance under five different temperatures. Our results suggest that thermal responses are relatively conserved along the phylogeny, as the locomotor performance and thermal windows for activity remained narrow in Eupsophus species when compared against results observed for Batrachyla taeniata and Rhinella spinulosa. Additionally, we found significant individual differences in locomotor performance within most species, with individual consistency in performance observed across varied temperatures. Further analyses explored the influence of body size on locomotor performance and critical thermal limits within and between species. Our results suggest a trade-off scenario between thermal tolerance breadth and locomotor performance, where species exhibiting broader thermal ranges might have compromised performance. Interestingly, these traits seem partly mediated by body size variations, raising questions about potential ecological implications.

Refinement of microneedles application – A comparative study regarding species variation in skin histology

Refinement of microneedles application – A comparative study regarding species variation in skin histology

Searching for common patterns in parasite ecology: species and host contributions to beta-diversity in helminths of South African ungulates and fleas of South American rodents

We searched for common patterns in parasite ecology by investigating species and host contributions to the beta-diversity of infracommunities (=assemblages of parasites harboured by a host individual) in helminths of three species of South African ungulates and fleas of 11 species of South American rodents, assuming that a comparison of patterns in distinctly different parasites and hosts would allow us to judge the generality or, at least, commonness of these patterns. We used data on species’ composition and numbers of parasites and asked whether (i) parasite species’ attributes (life cycle, transmission mode, and host specificity in helminths; possession of sclerotized combs, microhabitat preference, and host specificity in fleas) or their population structure (mean abundance and/or prevalence) and (ii) host characteristics (sex and age) affect parasite and host species’ contributions to parasite beta-diversity (SCBD and HCBD, respectively). We found that parasite species’ morphological and ecological attributes were mostly not associated with their SCBD. In contrast, parasite SCBD, in both ungulates and rodents, significantly increased with either parasite mean abundance or prevalence or both. The effect of host characteristics on HCBD was detected in a few hosts only. In general, parasite infracommunities’ beta-diversity appeared to be driven by variation in parasite species rather than the uniqueness of the assemblages harboured by individual hosts. We conclude that some ecological patterns (such as the relationships between SCBD and parasite abundance/prevalence) appear to be common and do not differ between different host-parasite associations in different geographic regions, whereas other patterns (the relationships between SCBD and parasite species’ attributes) are contingent and depend on parasite and host identities.

Where east meets west: Phylogeography of the high Arctic North American brant goose.

Genetic variation in Arctic species is often influenced by vicariance during the Pleistocene, as ice sheets fragmented the landscape and displaced populations to low- and high-latitude refugia. The formation of secondary contact or suture zones during periods of ice sheet retraction has important consequences on genetic diversity by facilitating genetic connectivity between formerly isolated populations. Brant geese (Branta bernicla) are a maritime migratory waterfowl (Anseriformes) species that almost exclusively uses coastal habitats. Within North America, brant geese are characterized by two phenotypically distinct subspecies that utilize disjunct breeding and wintering areas in the northern Pacific and Atlantic. In the Western High Arctic of Canada, brant geese consist of individuals with an intermediate phenotype that are rarely observed nesting outside this region. We examined the genetic structure of brant geese populations from each subspecies and areas consisting of intermediate phenotypes using mitochondrial DNA (mtDNA) control region sequence data and microsatellite loci. We found a strong east-west partition in both marker types consistent with refugial populations. Within subspecies, structure was also observed at mtDNA while microsatellite data suggested the presence of only two distinct genetic clusters. The Western High Arctic (WHA) appears to be a secondary contact zone for both Atlantic and Pacific lineages as mtDNA and nuclear genotypes were assigned to both subspecies, and admixed individuals were observed in this region. The mtDNA sequence data outside WHA suggests no or very restricted intermixing between Atlantic and Pacific wintering populations which is consistent with published banding and telemetry data. Our study indicates that, although brant geese in the WHA are not a genetically distinct lineage, this region may act as a reservoir of genetic diversity and may be an area of high conservation value given the potential of low reproductive output in this species.

The role of slope as an environmental variable in plant biodiversity change in Aegean rangelands by SHE analysis: The case of Çakmar rangeland

Rangelands, which have rich plant and animal biodiversity, are also very important as a source of roughage for livestock. Rangeland vegetation patterns vary considerably under the influence of environmental factors. Indicator factors need to be identified and analyzed in order to manage conservation and utilization objectives. In rangelands of the Aegean region, the slope factor can greatly affect the rangeland plant biodiversity in areas close to the base rangeland. In order to investigate the spatial distribution and species variation in plant biodiversity caused by slope, 6 rangeland sections with different slopes were sampled in Koçarlı region (Aydın / Türkiye). Sampling was carried out using the transect method in the spring 2017 based on field observations. Following sampling, indicator species and species distribution and abundance were determined. Alpha biodiversity indices were used to determine the change in species biodiversity by SHE analysis. SHE analysis tests the relationship between S (species richness), H (Shannon-Wiener diversity index) and E (equality). This method aims to examine the contribution of the number of species and the concept of equity in the context of diversity. According to the information obtained as a result of the analysis, it was seen that the increase in slope may cause a decrease in species biodiversity. More species diversity was found in rangelands with low base and slope. Factors such as erosion and water transport affect the canopy and species abundance in high slope rangelands. However, other factors such as grazing intensity can reverse this situation. For this purpose, it has been determined that slope is an important environmental variable when preparing management plans based on grazing capacity and grazing animal species in vegetation studies.

Variation and clustering analysis of several species of soursop family (Annonaceae) based on vegetative morphology characters

The Annonaceae family exhibited a high level of diversity and is spread over many regions. The designation of the names of several species of the Annonaceae family varies in each region. Therefore, characterization is needed to confirm and classify the taxonomy position of the species. This study aims to characterize the variation and analyze the clustering pattern of several species of the Annonaceae based on vegetative morphology characters. The type of method used in this research is exploratory descriptive, with seventeen specimen species consisting of ten Annonaceae studied in this research. Characters observed include tree age, stem diameter, plant height, stem color, type of sapling, type of branching, leaf shape, leaf tip shape, leaf base shape, leaf width, leaf length, leaf thickness, petiole length and thickness, leaf hairs , color of young and mature leaves, type of leaf edge, number of leaf veins, color of young branches, leaf hairs on young branches, and number of nodes on the stem per meter. These qualitative and quantitative characters were observed using Descriptors for Cherimoya (Annona cherimola Mill.) from Bioversity International and CHERLA. Data analysis was conducted in the Paleontological Statistics program with cluster analysis method (Bray-curtis similarity index) to produce a dendrogram topology. Results showed that there were variations in vegetative morphological characteristics among the ten species examined. Dendrogram topology was divided into 3 groups relatively following the tribe division, with similarity index 0.64 to 0.96. Xylopia sp. was separated from the others in Group 1 (Xylopiae). Group 2 (Uvariae) consisted of Fissistigma sp., Desmos chinensis, Artabotrys suaveolens, Uvaria purpurea, and Desmos sp. Group 3 (Annoneae) consisted of Annona muricata, Annona montana, Stelechocarpus burahol, and Annona glabra. Vegetative morphological characters have proven to be useful and effective in differentiating species in the Annonaceae family; it is recommended for initial identification of species, especially in the Annonoideae subfamily.

Selective oxygen-doping in self-supportive carbon electrode by electrochemical oxidation for electrocatalytic synthesis of hydrogen peroxide

We report the selective introduction of oxygen-containing functional groups for two-electron oxygen reduction reaction (2e-ORR) in self-supportive carbon electrode using electrochemical oxidation method. The optimal electrode shows hydrogen peroxide (H2O2) selectivity up to 95 %. CO is found active to control 2e-ORR selectivity and mechanism of oxygen species variation is elucidated by in situ infrared reflection absorption spectroscopy. We further improve mass transfer by introducing highly interconnected macropores in electrode, which shows H2O2 yield of 144 mmol cm−2 h−1 and Faradaic efficiency of nearly 100 %. These may inspire advanced active electrode creation for applications through selective electrochemical doping and structural design.

Assessing Pollinator Assembly And Efficacy Across Species Ranges In The Genus Triodanis (Campanulaceae)

Plant-insect interactions are a key topic in evolutionary ecology, especially in the face of anthropogenic changes which threaten to disrupt these mutualisms. An in-depth pollinator survey for species in the genus Triodanis is performed here for the first time, with sampling covering four species and spanning a large portion of their geographic ranges (i.e., four U.S. states). All species in the genus exhibit dimorphic cleistogamy with variability in allocation to open (chasmogamous) flowers among populations and taxa. The genus Triodanis, therefore, provides an opportunity for understanding possible associations between pollinator assemblies and variation in species, breeding system, and geography. To assess these relationships, we sampled four species or subspecies of Triodanis at eight field sites in four states. Sampling encompassed a broad area across the Midwestern U.S. and Texas, and across a gradient of anthropogenically disturbed habitats. We found that for species of Triodanis: 1) small bee and fly generalist pollinators showed some floral constancy during feeding bouts but did not differentiate between species, 2) pollinator community was less diverse and abundant in highly degraded habitats, 3) while allocation to open flowers varied among species and populations, we found no association between breeding system (or species) on pollinator identity or abundance. This study represents the first in-depth survey of pollinator visitors of Triodanis and serves as foundational knowledge about the natural history of this group, provides resolution for members of Campanulaceae exhibiting floral traits of generalist hosts, and important documentation of plant-insect interactions in an era of ongoing anthropogenic changes.

Primary study on frass fertilizers from mass-reared insects: Species variation, heat treatment effects, and implications for soil application at laboratory scale

Insect farming has gained popularity as a resource-efficient and eco-friendly method for managing organic wastes by converting them into high-quality protein, fat, and frass. Insect frass is a powerful organic fertilizer that enriches the soil with essential plant nutrients and enhances plant defense mechanisms through chitin stimulation. Given the importance of frass commercialization for many insect farmers and the use of increasingly diverse organic wastes as insect feedstocks, there is a need for legal guidelines to enable clean production practices. The recent introduction of a legal definition for frass and heat treatment requirements by the EU commission marks a significant step towards standardizing its quality; however, little is known about the processes shaping its nutritional profiles and contributing to its maturation. Our study addresses key knowledge gaps in frass composition and production practices. Here, we analyzed the physicochemical, plant-nutritional, and microbiological properties of black soldier fly, yellow mealworm, and Jamaican field cricket frass from mass-rearing operations and assessed the impact of hygienizing heat treatment on fertilizer properties and frass microbiota. The results showed that frass properties varied significantly across insect species, revealing concentrations of plant-available nutrients as high as 7000 μg NH4+-N, 150 μg NO2–NO3--N, and 20 mg available P per g of total solids. Heat treatment reduced microbial activity, biomass, and viable counts of pathogenic Escherichia coli and Salmonella spp. In terms of frass microbiome composition, alpha diversity showed no significant differences between fresh and heat-treated frass samples; however, significant differences in microbial community composition were observed across the three insect species. Despite heat treatment, soil application of frass reactivated and boosted soil microbial activity, inducing up to a 25-fold increase in microbial respiration, suggesting no long-term detrimental effects on microorganisms. These findings not only enhance our understanding of insect frass as a nutrient-rich organic fertilizer but also have implications for regulatory frameworks, underscoring its promising potential for soil health and nutrient cycling. However, it is important to recognize the primary nature of this research, conducted at laboratory scale and over a short term. Future studies should aim to validate these findings in agricultural settings and explore additional factors influencing frass properties and its (long-term) interaction with soil ecosystems.

Weed Species’ Diversity and Composition as Shaped by the Interaction of Management, Site, and Soil Variables in Olive Groves of Southern Greece

Gaining a comprehensive understanding of how weed communities respond to both environmental and human-induced factors is of paramount importance in developing effective and ecologically sound weed control strategies. The objectives of the current research were to (1) assess the effect of the main weed management practices used in Greek olive groves on weed species’ diversity; (2) explore the filtering effect of management, site, and soil variables in determining weed species’ composition; and (3) shed light on the association between weed species’ composition and the diversity of the understory vegetation of olive groves. To accomplish these objectives, winter weed species’ coverage was assessed in 116 olive groves, both conventional and organic, distributed across three provinces in southern Greece. The investigation encompassed 29 explanatory variables, categorized into three groups: soil (22), management practices (6), and site conditions (1). It was confirmed that glyphosate use may lower biodiversity and species richness; however, this trend was not universal. In fact, the negative influence of the presence of Oxalis pes-caprae L. on species richness and diversity far outweighed the effect of spraying glyphosate. Redundancy analysis (RDA) revealed that among the 29 variables used to describe the ecological niche, eight (i.e., Mn, Mg, chemical spraying, mowing, rotary tiller, grazing, irrigation, and elevation) were significant and explained 21.5% of the total variation in weed species’ data. Interestingly, the soil Mn concentration was identified as the most influential one, highlighting the importance of soil micronutrients in determining weed species’ composition. The variation partitioning procedure demonstrated that the effect of the management variables on weed species’ composition accounted for 2.2 times the variance of soil variables and 4.5 times the variance of elevation. The present findings might help to enhance optimal management in olive groves that can sustain the biodiversity of flora and, in turn, provide various ecosystem services to agro-ecosystems.