Variation In Populations Research Articles

A climate analog approach to evaluate seed transfer and vegetation transitions

IntroductionThere is growing recognition that restoring species diversity is crucial to maintaining ecological functions and services. Increasing the diversity of species used in restoration programs has placed greater emphasis on determining the seed transfer needs for a wider array of plants. However, many plants, outside of commercial forestry, lack information that would provide guidance on seed transfer for current or future climates. Generalized seed transfer approaches use climate partitioning to approximate adaptive differentiation among populations and provide an estimation of seed transfer distance for such species.MethodsHerein, we describe a generalized seed transfer approach that uses Euclidean distance of 19 climate variables within North America (from northern Honduras to the Arctic). Euclidean distances are used to identify climate analogs from vegetation databases of about 685,000 plots, an average density of 1 plot per 32 km2. Analogs are classified into three thresholds (strong, moderate, and weak) that correspond to altitudinal climate gradients and are guided by the scientific literature of observed adaptive variation of natural tree populations and seed transfer limits.ResultsFor strong threshold observations, about 97% of the analogs had climate distances equivalent to ≤300 m elevation, whereas for the weak threshold observations, 53% had an elevation equivalence of ≤300 m. On average 120, 267, and 293 m elevation separated two points under strong, moderate, and weak thresholds, respectively. In total, threshold classification errors were low at 13.9%.DiscussionWe use examples of plot data identified from a reference period (1961–1990) and mid-century (2056–2065) analogs across North American biomes to compare and illustrate the outcomes of projected vegetation change and seed transfer. These examples showcase that mid-century analogs may be located in any cardinal direction and vary greatly in spatial distance and abundance from no analog to hundreds depending on the site. The projected vegetative transitions will have substantial impacts on conservation programs and ecosystem services. Our approach highlights the complexity that climate change presents to managing ecosystems, and the need for predictive tools in guiding land management decisions to mitigate future impacts caused by climate change.

Review of Phenotypic Heterogeneity of Neuronal Intranuclear Inclusion Disease and NOTCH2NLC-Related GGC Repeat Expansion Disorders.

Neuronal intranuclear inclusion disease (NIID) is an underdiagnosed neurodegenerative disorder caused by pathogenic GGC expansions in NOTCH2NLC. However, an increasing number of reports of NOTCH2NLC GGC expansions in patients with Alzheimer disease, essential tremor, Parkinson disease, amyotrophic lateral sclerosis, and oculopharyngodistal myopathy have led to the proposal of a new concept known as NOTCH2NLC-related GGC repeat expansion disorders (NREDs). The majority of studies have mainly focused on screening for NOTCH2NLC GGC repeat variation in populations previously diagnosed with the associated disease, subsequently presenting it as a novel causative gene for the condition. These studies appear to be clinically relevant but do have their limitations because they may incorrectly regard the lack of MRI abnormalities as an exclusion criterion for NIID or overlook concomitant clinical presentations not typically observed in the associated diseases. Besides, in many instances within these reports, patients lack pathologic evidence or undergo long-term follow-up to conclusively rule out NIID. In this review, we will systematically review the research on NOTCH2NLC 5' untranslated region GGC repeat expansions and their association with related neurologic disorders, explaining the limitations of the relevant reports. Furthermore, we will integrate subsequent studies to further demonstrate that these patients actually experienced distinct clinical phenotypes of NIID.

Elastic Shape Analysis of Tree-Like 3D Objects Using Extended SRVF Representation.

How can one analyze detailed 3D biological objects, such as neuronal and botanical trees, that exhibit complex geometrical and topological variation? In this paper, we develop a novel mathematical framework for representing, comparing, and computing geodesic deformations between the shapes of such tree-like 3D objects. A hierarchical organization of subtrees characterizes these objects - each subtree has a main branch with some side branches attached - and one needs to match these structures across objects for meaningful comparisons. We propose a novel representation that extends the Square-Root Velocity Function (SRVF), initially developed for Euclidean curves, to tree-shaped 3D objects. We then define a new metric that quantifies the bending, stretching, and branch sliding needed to deform one tree-shaped object into the other. Compared to the current metrics such as the Quotient Euclidean Distance (QED) and the Tree Edit Distance (TED), the proposed representation and metric capture the full elasticity of the branches (i.e., bending and stretching) as well as the topological variations (i.e., branch death/birth and sliding). It completely avoids the shrinkage that results from the edge collapse and node split operations of the QED and TED metrics. We demonstrate the utility of this framework in comparing, matching, and computing geodesics between biological objects such as neuronal and botanical trees. We also demonstrate its application to various shape analysis tasks such as (i) symmetry analysis and symmetrization of tree-shaped 3D objects, (ii) computing summary statistics (means and modes of variations) of populations of tree-shaped 3D objects, (iii) fitting parametric probability distributions to such populations, and (iv) finally synthesizing novel tree-shaped 3D objects through random sampling from estimated probability distributions.

Role of Omega 3 Fatty Acid as an Adjunct Treatment to Depression in Different Age Groups of the Patient Population - A Current Literature Review

IntroductionDepression is a widespread problem that affects individuals of all ages. This study looks at the use of omega-3 polyunsaturated fatty acids (PUFAs) as an additional therapy for depression in people of different ages. Depression has an impact on everyone, from youth to the elderly, causing therapeutic concerns such as treatment resistance and recurrence. Omega-3 PUFAs, which may be found in fish and flaxseed, are important because of their impact on neurochemistry, inflammation, and neuroprotection. While pharmacotherapy, including antidepressants, has proven beneficial for many, the likelihood of remission and recurrence remains substantial. In recent years, there has been a growing interest in the potential role of omega-3 polyunsaturated fatty acids (n-3 PUFAs) in mitigating depressive symptoms. The primary constituents of n-3 PUFAs are eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Understanding the potential of omega-3 PUFAs across the lifespan can help address the multifaceted challenges posed by depression and improve mental health outcomes for diverse age groups.ObjectivesThis review aims to assess the role of omega-3 fatty acids in depression treatment across different age groups: children and adolescents, adults (18–60), and the elderly (60+). It investigates the effectiveness and potential differences in omega-3 supplementation among these age cohorts.MethodsA comprehensive literature search was conducted from 2003 to 2023 using PubMed, Google Scholar, and EMBASE, using specific keywords. Studies with inadequate age group information or Omega-3 intervention were excluded.Results In children and adolescents, several studies indicate a positive association between omega-3 supplementation and improved depressive symptoms. In adults, results are mixed, with some studies showing benefits while others do not. In the elderly, omega-3 PUFAs appear to have a more consistent positive effect on depression. In contrast, a consistent positive association was observed in the geriatric population, suggesting that Omega-3 PUFAs may hold particular promise in the treatment of depression among older adults. However, variations in methodology, dosage, and study populations contribute to these mixed findings.ConclusionsOmega-3 PUFAs show promise as an adjunct therapy for depression across different age groups. Further research with standardized methodologies and larger sample sizes is needed to clarify their role and establish optimal dosage guidelines. Omega-3 PUFAs should be considered as a potential complement to conventional depression treatments, emphasizing the need for personalized approaches in depression management.Disclosure of InterestNone Declared

Analysis of the Association of IL-1A, IL-1B, and IL-1RN Genetic Polymorphisms with Peri-implantitis in a Portuguese Population.

To investigate whether genetic variations in cytokine genes involved in the pathogenesis of peri-implantitis are associated with the occurrence of peri-implantitis, an issue that remains controversial and may vary according to the population evaluated. A cross-sectional analytical study was carried out on 102 Caucasian Portuguese individuals who were divided into two groups: (1) 43 individuals with peri-implantitis and (2) 59 individuals with good peri-implant health. Samples from the buccal mucosa were obtained, and genetic analysis was performed using the real-time polymerase chain reaction (PCR) technique for IL-1A and IL-1B and PCR for IL-1RN. The IL-1A-889 C/T polymorphism presented with a higher prevalence of the less common allele (T allele) in patients with peri-implantitis (27.9%) than in healthy patients (16.9%), but without statistical significance (P = .060). For the IL-1B+3954 C/T and IL-1RN (variable number of tandem repeats [VNTR]) polymorphisms, analysis revealed that the allele and genotype frequencies did not differ significantly between groups. There was a significant association between a history of periodontitis and peri-implantitis (P = .020). The evaluated genetic polymorphisms had no influence on the occurrence of peri-implantitis in the study population. Further research into genetic variations in different populations is needed to elucidate the role of genetic factors in the onset and progression of peri-implant disease.

The Bacterial and Fungal Compositions in the Rhizosphere of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. in a Typical Planting Region.

Asarum is a traditional Chinese medicinal plant, and its dried roots are commonly used as medicinal materials. Research into the traits of the bacteria and fungus in the Asarum rhizosphere and how they relate to the potency of medicinal plants is important. During four cropping years and collecting months, we used ITS rRNA gene amplicon and sequencing to assess the population, diversity, and predominant kinds of bacteria and fungus in the rhizosphere of Asarum. HPLC was used to determine the three bioactive ingredients, namely asarinin, aristolochic acid I, and volatile oil. The mainly secondary metabolites of Asarum, relationships between microbial communities, soil physicochemical parameters, and possible influences on microbial communities owing to various cropping years and collecting months were all statistically examined. The cropping years and collecting months affected the abundance and diversity of rhizosphere bacteria and fungi, but the cropping year had a significant impact on the structures and compositions of the bacterial communities. The rhizosphere microorganisms were influenced by both the soil physicochemical properties and enzyme activities. Additionally, this study revealed that Trichoderma was positively correlated with the three bioactive ingredients of Asarum, while Tausonia showed entirely opposite results. Gibberella and Leptosphaeria demonstrated a significantly negative correlation with asarinin and violate oil, but they were weakly correlated with the aristolochic acid I content. This study revealed variations in the Asarum rhizosphere microorganism population, diversity, and dominant types across four cropping years and collecting months. The relationship between Asarum secondary metabolites, the soil physicochemical properties, enzyme activities, and rhizosphere microorganisms was discussed. Our results will guide the exploration of the soil characteristics and rhizosphere microorganisms' structures by regulating the microbial community to enhance Asarum quality.

Parasitic nematode populations associated with developmental stages of mango in production regions of Ghana

Nematode (Phylum nematoda) infestation is a major set back in mango (Mangifera indica) production world-wide. Control of nematodes requires understanding of their diversity, distribution and population densities. The objective of this study was to identify plant-parasitic nematodes associated with mangoes and their population densities at seedling and maturity stages in production regions of Ghana. The study was conducted in Greater Accra (Manya and Klagon) and the Eastern region (Somanya) during December 2016 to January 2018. Mango farmlands were surveyed for soil and root samples, from which nematodes were extracted, identified and quantified. Twenty-four nematode genera were identified in mango seedlings and matured trees from Somanya; and 14 genera dentified in seedlings and 22 in matured trees from Manya; while at Klagon, 15 nematode genera were identified in matured trees. Helicotylenchus spp. were the most populated in seedlings obtained from Somanya and Manya, with relative abundance of 23.29%. Tylenchus spp. had the highest population in mature trees, with relative abundance of 24.49% at Somanya and 38.86% at Manya; while Helicotylenchus spp. had the highest relative abundance of 43.96% at Klagon. Mature trees had higher nematode population densities, compared to seedlings. There were significant variation in nematode populations between seedlings and matured stages of mango.

Magnetic Resonance Imaging (MRI) Insights into Brain Morphology and Connectivity Disruptions in Schizophrenia

This review explores the transformative impact of Magnetic Resonance Imaging (MRI) on understanding schizophrenia. Structural MRI has unveiled significant alterations in brain regions like the hippocampus and prefrontal cortex, offering detailed insights into anatomical irregularities. Functional MRI studies have shed light on disruptions within the default mode network, providing valuable insights into cognitive deficits associated with the disorder. Additionally, Diffusion Tensor Imaging has highlighted white matter abnormalities, underscoring compromised interregional communication within the brain. Despite persistent challenges such as population heterogeneity and variations in imaging protocols, MRI techniques have significantly advanced our understanding of schizophrenia's neurobiological aspects.

Vector mosquito distribution and richness are predicted by socio-economic, and ecological variables

Mosquitoes of vectorial importance represent a ubiquitous and constant threat of potentially devastating arboviral outbreaks. Our ability to predict such outcomes is still restricted. To answer this, we have used an extensive data collection of 23 vector and 233 non-vector mosquito species distributed throughout the Mexican territory and linked them to social and environmental factors. Our aim was to predict vector and non-vector mosquitoes’ distribution and species richness based on socioeconomic and environmental data. We found that lack of health services, human population variation, ecological degradation, and urban-rural categorization contributed significantly to explain the distribution of vector mosquitoes. mosquitoes. This phenomenon is probably attributed to the degradation of natural ecosystems as it creates favorable conditions for the proliferation of vector mosquitoes. The richness of vector mosquitoes was similarly explained by most of these variables as well as altitude. As for non-vector mosquitoes, social marginalization, ecological degradation, anthropogenic impact, and altitude explain species richness and distribution. These findings illustrate the complex interaction of environmental and socioeconomic factors behind the distribution of mosquitoes, and the potential for arboviral disease outbreaks. Areas with human populations at highest risk for mosquito-borne diseases should be primary targets for vector control.

Evolution of individual variation in a competitive trait: a theoretical analysis.

When competitive traits are costly, negative frequency dependence can maintain genetic variance. Most theoretical studies examining this problem assume binary polymorphisms, yet most trait variation in wild populations is continuous. We propose that continuous trait variation can result from continuous variation in resource quality and that, specifically, the shape of the resource distribution determines trait maintenance. We used an individual-based model to test which conditions favour the stable maintenance of variation and which cause temporal fluctuations in trait values. This approach, inspired by contrasting outcomes of previous studies regarding variance and fluctuations in trait values, clearly showed a decisive role played by the shape of resource distributions. Under extreme conditions, e.g., the absence of resource variation or with very scarce resources for weak competitors, traits evolved to a single non-competitive or highly competitive strategy, respectively. Most other distributions led to strong temporal fluctuations on trait values or the maintenance of stable, standing variation. Our results thus explain the contradicting outcomes of previous theoretical studies and, at the same time, provide hypotheses to explain the maintenance of genetic variation and individual differences. We suggest ways to empirically test the proposed effects of resource variation on trait maintenance.

Genetic diversity, population structure and origin of the native goats in Central Laos.

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village-based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011-0.043) and negligible inbreeding coefficients (FIS: -0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92-6.85 Mb, with short ROH segments (1-5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20-40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low-inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features.

Abstract 7292: Surveying the landscape of somatic variation in healthy breast tissue for cancer risk prediction

Abstract Carcinogenesis centers on principles of somatic evolution, where a cell gradually accumulates mutations, eventually transforming into a tumor cell. Exploring somatic variation in the healthy population offers insights for predicting cancer risk and facilitating early detection. In breast cancer (BC), the emergence of the malignant clone occurs within a broader spectrum of abnormal cells, often referred to as the 'field effect.' BC development is intricately linked to hormonal regulation, with prior research indicating that the initial changes manifest during puberty and pregnancy. Although around 10% of diagnosed BCs affect young women (<45 years), with 35-55% of these cases arising within a decade after completed pregnancy (postpartum BC), effective screening tools are lacking. We propose a novel approach for the individualized quantification of somatic variation and the field effect using breast milk (BM) as a liquid biopsy. We conducted a retrospective analysis of 272 BM samples obtained from both the left and right breasts of 125 healthy donors, including 62 donors with elevated cancer risk due to a germline predisposition involving BRCA. Given the heterogeneous cellular composition of BM, encompassing epithelial cells and lymphocytes, we initially implemented a comprehensive analysis to reliably detect somatic mutations in whole BM, as well as in magnetically activated cell-sorted (MACS) epithelial-enriched (EE) and -depleted (ED) samples from a subset of donors. DNA extracted from all samples was used for NanoSeq, a single-molecule sequencing methodology, focusing on a targeted panel of 84 genes recognized as drivers in either BC or normal tissue. Our assessment of mutation burden estimates across all sample types revealed consistent results. Generally, cells accumulated somatic mutations linearly with age, but with a higher rate in individuals with a BRCA2 cancer predisposition. We found several critical driver genes, including PIK3CA, PIK3R1, TP53, to be under significant positive selection using the ratio of non-synonymous to synonymous mutations. When we assessed the fraction of cells in each sample carrying mutations in these genes, we however detected a significantly higher fraction of mutated cells in individuals with germline predisposition - possibly representing a genetic manifestation of the epidemiologically higher risk of BRCA germline carriers. As we expand our understanding of the interplay between the somatic mutation landscape and cancer risk, our efforts provide evidence for the utility of BM as an easily accessible, non-invasive sample. The proposed methodology, involving BM with precise genetic analysis through NanoSeq, presents a promising avenue for elucidating personalized somatic variation patterns. We anticipate that BM holds potential as a valuable tool for risk stratification, particularly for individuals under 45 and postpartum women. Citation Format: Moritz Jakob Przybilla, Andrew R. Lawson, Pantelis Nicola, Brian T. Pentecost, Inigo Martincorena, Kathleen F. Arcaro, Peter J. Campbell. Surveying the landscape of somatic variation in healthy breast tissue for cancer risk prediction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7292.

Abstract 5335: Immune cell population variations in the livers of commonly used mouse strains

Abstract Previous studies have shown that the distribution of major immune cell populations differ across mouse strains in peripheral blood and hematopoietic organs at baseline. Additionally, variations in immune responses exist between mouse strains in Leishmania spp. and Melanoma models, but these studies in the context of liver diseases including Non Alcoholic Fatty Liver Disease (NAFLD) and Hepatocellular Carcinoma (HCC) have not been carried out. With the effort to state if these variations exist within the liver, we performed comprehensive spectral flow cytometry analysis on the liver and spleens of three female mouse strains commonly used in cancer research (BALB/c, C57BL/6, and FVBN). NAFLD was induced by providing mice with a methionine choline deficient diet. To promote HCC, a single genotype (myc/p53+/-) was induced by administering transposon-based vectors to overexpress Myc-Luc and CRISPR/Cas-9 vectors to knock down p53 via hydrodynamic tail-vein injection. To confirm vector integration and monitor tumor growth (luciferase activity), in vivo imaging was performed at different time points. As a result, we confirm throughout this study that differences exist within immune cell populations of the liver and spleen at baseline. Moreover, we depict differences in the shift of immune cell populations across mouse strains in the pathologic states included. In NAFLD, there is an increase of dendritic cells (DCs), macrophages, NK cells, ILC1s, T regulatory cells (Tregs), TH1, and TH2, and a decrease of CD4+ T cells, B cells, γδ-T cells, and NKT cells in the liver across all mouse strains, when compared to controls. However, the population of neutrophils in BALB/c decreases, and the population of CD8+ T cells increases in C57BL/6 mice, which differs from the patterns of change seen in the other mouse strains. Moreover, in spleens, NAFLD promotes an increase of TH1 and NK cells, and a decrease of TH2 and NKT Cells across the mouse strains included in the study, whereas the patterns of change differ between mouse strains among the remaining immune cell types. When evaluating liver immune cell population shifts on our HCC model, BALB/c mice showed a decrease in macrophages and ILC1s, C57BL/6 mice showed a decrease in γδ-T cells, prominent shifts across Neutrophils, TH1, and NKT cells, and null changes in TH2 and CD4+ T cell shifts, and FVBN mice had a less prominent decrease of B cells, which differed from the shifts observed in the mouse strains used for comparison. Immune cell populations in the spleens of our HCC mouse model also presented with differences across the mouse strains studied. In conclusion, we highlight that key differences in immune profiles exist across commonly used mouse strains for cancer research in the presence of liver pathology including HCC, suggesting that mouse strains could be possible confounders in the study of immune oncology of HCC. Citation Format: Francisco J. Rodriguez-Matos, Patrick Huang, Rajiv Trehan, Benjamin Ruf, Chi Ma, Tim F. Greten. Immune cell population variations in the livers of commonly used mouse strains [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5335.

Genetic Variation of Foxtail Millet (Setaria italica (L.) P. Beauv.) Germplasm From Polewali Mandar West Sulawesi Based On Morphological Characters

Foxtail millet (Setaria italica (L.) P. Beauv.) is a cereal crop that has long been domesticated worldwide and has been adopted as a model crop to provide a deeper understanding of plant biology. This plant has long been a mainstay of indigenous Indonesian people, especially in Polewali Mandar, West Sulawesi Province. This study aims to evaluate the genetic variation of foxtail millet germplasm from Polewali Mandar, West Sulawesi based on morphological characters. Three germplasm populations were collected from Polewali Mandar to assess genetic variation in millet germplasm. The observations of morphological traits were carried out based on the IBPGR of Setaria italica. Genetic variation in foxtail millet populations was measured using 28 morphological traits with nine qualitative and 19 quantitative characters. The research showed that seed color, stem diameter, plant height, panicle stalk length, and panicle stalk diameter had diverse variations. Cluster analysis of morphological characters using the UPGMA method shows a similarity coefficient ranging from 0.15-0.2. At a genetic similarity coefficient of 0.2, the three populations were divided into Cluster A and Cluster B. Cluster A consists of two populations (Minna' and Lasse'). In contrast, Cluster B consists of one population (Bulawang). The millet population SLB.C.3-SLB.A.1 has the highest genetic distance and is a potential candidate to be selected as a parent cross to produce higher het-erosis. Intensification of millet plant breeding programs is expected to increase the genetic basis for determining specific characteristics.

Evaluation of drone surveys for ungulates in southwestern rangelands

AbstractDrone platforms are increasingly used for aerial wildlife surveys, but the validity of population counts has not been fully evaluated in all environments. Aerial surveys generally undercount the true population size and one must estimate detection probability (p) to correct for missed individuals. Detection probability for visual observers is influenced by vegetation and terrain characteristics, but the use of thermal cameras as the observer may also introduce additional factors influencing detection probability. We conducted diurnal, thermal‐based drone surveys for ungulates during February–April 2020 in South Texas, USA, on sites with varying degrees of woody cover and terrain. We examined histograms of georeferenced perpendicular distances to determine the effect of habitat on detection probabilities. We also examined precision in population estimates and variation in repeated surveys. Finally, we compared drone population estimates to independent estimates derived from helicopter, spotlight, and trail‐camera surveys. Distributions of perpendicular distances from the transect were affected by habitat characteristics. A flat grassland site had relatively few detections near the transect because thermal (solar) reflectance in the center of the footage obscured detections. A hilly brushy site had a uniform p (1.00) but resulted in a severe undercount due to the inability of the drone to follow contours of hills. The flat brushy site had a lower p (0.63), indicating visibility bias. Two additional flat, brushy sites were surveyed repeatedly (n = 5 and 9 surveys, respectively). All combinations of up to 3 repeated surveys were pooled to meet the recommended minimum number of detections for distance sampling analyses (≥60 detections). Population estimates had acceptable precision (CV ≤ 20%) 80.7% of the time and variation among repeated surveys was acceptable (CV = 9% and 23%, respectively). Drone‐based population estimates were comparable with estimates generated from corrected helicopter, spotlight, and trail‐camera surveys. Overall, diurnal drone surveys can generate population estimates for large ungulates on southwestern rangelands after accounting for visibility bias, but may be limited by terrain and thermal conditions.

Landscape genomics reveals regions associated with adaptive phenotypic and genetic variation in Ethiopian indigenous chickens.

Climate change is a threat to sustainable livestock production and livelihoods in the tropics. It has adverse impacts on feed and water availability, disease prevalence, production, environmental temperature, and biodiversity. Unravelling the drivers of local adaptation and understanding the underlying genetic variation in random mating indigenous livestock populations informs the design of genetic improvement programmes that aim to increase productivity and resilience. In the present study, we combined environmental, genomic, and phenotypic information of Ethiopian indigenous chickens to investigate their environmental adaptability. Through a hybrid sampling strategy, we captured wide biological and ecological variabilities across the country. Our environmental dataset comprised mean values of 34 climatic, vegetation and soil variables collected over a thirty-year period for 260 geolocations. Our biological dataset included whole genome sequences and quantitative measurements (on eight traits) from 513 individuals, representing 26 chicken populations spread along 4 elevational gradients (6-7 populations per gradient). We performed signatures of selection analyses ([Formula: see text] and XP-EHH) to detect footprints of natural selection, and redundancy analyses (RDA) to determine genotype-environment and genotype-phenotype-associations. RDA identified 1909 outlier SNPs linked with six environmental predictors, which have the highest contributions as ecological drivers of adaptive phenotypic variation. The same method detected 2430 outlier SNPs that are associated with five traits. A large overlap has been observed between signatures of selection identified by[Formula: see text]and XP-EHH showing that both methods target similar selective sweep regions. Average genetic differences measured by [Formula: see text] are low between gradients, but XP-EHH signals are the strongest between agroecologies. Genes in the calcium signalling pathway, those associated with the hypoxia-inducible factor (HIF) transcription factors, and sports performance (GALNTL6) are under selection in high-altitude populations. Our study underscores the relevance of landscape genomics as a powerful interdisciplinary approach to dissect adaptive phenotypic and genetic variation in random mating indigenous livestock populations.

Beyond the dominant narratives: Identifying Indigenous and African individuals in Quebec St-Lawrence Valley colonial cemeteries by three-dimensional morphometrical analysis of the temporal bone

In Quebec, written accounts of free or enslaved Indigenous and African individuals during colonial times are few and limited. Three-dimensional geometric morphometric methods applied on 214 temporal bones individuals are used to explore intra-cemetery population variation throughout three centuries (1683–1878), to identify plausible non-European or admixed individuals. First, Principal Component Analysis (PCA) was generated from populations originated from Africa, North-America (Indigenous) and Europe where colonial cemeteries are projected to assess their degree of overlap with the reference groups. Second, Discriminant Function Analysis (DFA) based on typicality probabilities also allowed to assign unknown individuals to the three reference groups. Our results highlighted discrepancy between PCA and DFA. With the PCA, Quebec colonial groups overlap with the Europeans except for three individuals. For the DFA, 64 % (n = 136) were classified as typical to one group and 36 % as atypical (n = 77). Most were European, (82 %; n = 112), followed by those as Indigenous (7 %; n = 10), intermediate between Africans and Indigenous (6 %; n = 8) and Africans (5 %; n = 7). Compared with previous research, one individual from the first Protestant cemeteries of St-Matthew in Quebec could be assessed as plausible African or admixed origin. Two others need further analysis: one from St-Matthew and one from the first Catholic cemetery of Notre-Dame in Montreal. Finally, in response to dominant narratives that focused mainly on Euro-colonists, this research provided for the first time a new snapshot of several colonial population diversity in Quebec, underlining the presence of marginalized groups -especially those of African origin, who are absent from the archaeological reports under study.

Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.

Exploring Land Use/Land Cover Dynamics and Statistical Assessment of Various Indicators

Current information on urban land use and surface cover is derived from the land classification of cities, facilitating accurate future urban planning. Key insights are driven by multi-year remote sensing data. These data, when analyzed, produce high-resolution changes on the Earth’s surface. In this context, publicly accessible Urban Atlas data are employed for the high-precision and high-resolution classification and monitoring of terrestrial surfaces. These datasets, which are useful for preserving natural resources, guiding spatial developments, and mitigating pollution, are crucial for monitoring changes and managing cities. This research aims to analyze and contrast land use and land cover (LULC) changes in Gaziantep (Turkey) between 2010 and 2018 using Urban Atlas data, and to investigate correlations between the city’s statistical data and LULC changes. Gaziantep’s urban dynamics were analyzed using Urban Atlas datasets from 2010 to 2015 and 2012 to 2018, the latter part of Copernicus, the European Earth Observation Programme. To understand the impact of LULC changes on urban landscapes, people, and the environment, official environmental and demographic statistics spanning four years were sourced and studied. The findings reveal a trend of agricultural and vacant lands evolving into residential and industrial zones, with such changes likely to increase in the near future, given the growth of building zones. While some land classes have shown consistent area values annually, residential and industrial zones have expanded in response to housing and employment demands. The most significant alterations have occurred in the last three years. Shifts in urban configurations align closely with migratory patterns, reflecting notable variations in factors like population, consumption, and pollution.

Ecological characteristics explain neutral genetic variation of three coastal sparrow species.

Eco-phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species-specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co-distributed saltmarsh sparrow species differing along a specialization gradient-Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco-phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long-term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist-generalist status and support the role of an eco-phylogeographic approach in population and conservation genetics.