Natural Populations Research Articles

Risk Assessments and Risk Mitigation to Prevent the Introduction of African Swine Fever into the Danish Pig Population.

African Swine Fever poses a significant threat to pig production. An outbreak in Denmark would have severe economic consequences, potentially resulting in a loss between 335 million and 670 million euros. To mitigate the major risk factors, the Danish authorities and the Danish pig industry have implemented several risk-reducing measures. The small wild boar population in Danish nature has been culled, and a fence between Denmark and Germany has been constructed to stop or reduce the risk of migrating wild boar from Germany. All trucks arriving from abroad, intended for the transport of Danish pigs, are inspected, washed, and disinfected at facilities near the border before being allowed to transport pigs between herds or from herds out of Denmark. Cross-border trade of feedstuffs and potentially risky materials is continuously monitored. Based on risk assessments, feed types or bedding materials from countries with African Swine Fever that could contain parts of wild boar are banned from Danish pig herds. Certain types of fats and oils from countries with African Swine Fever can only be used after heat treatment. The import of whole kernels of corn, wheat, or barley is not considered a risk.

Heritable intraspecific variation among prey in size and movement interact to shape predation risk and potential natural selection

Abstract Predator and prey traits are important determinants of the outcomes of trophic interactions. In turn, the outcomes of trophic interactions shape predator and prey trait evolution. How species' traits respond to selection from trophic interactions depends crucially on whether and how heritable species' traits are and their genetic correlations. Of the many traits influencing the outcomes of trophic interactions, body size and movement traits have emerged as key traits. Yet, how these traits shape and are shaped by trophic interactions is unclear, as few studies have simultaneously measured the impacts of these traits on the outcomes of trophic interactions, their heritability, and their correlations within the same system. We used outcrossed lines of the ciliate protist Paramecium caudatum from natural populations to examine variation in morphology and movement behaviour, the heritability of that variation, and its effects on Paramecium susceptibility to predation by the copepod Macrocyclops albidus. We found that the Paramecium lines exhibited heritable variation in body size and movement traits. In contrast to expectations from allometric relationships, body size and movement speed showed little covariance among clonal lines. The proportion of Paramecium consumed by copepods was positively associated with Paramecium body size and velocity but with an interaction such that greater velocities led to greater predation risk for large body‐sized paramecia but did not alter predation risk for smaller paramecia. The proportion of paramecia consumed was not related to copepod body size. These patterns of predation risk and heritable trait variation in paramecia suggest that copepod predation may act as a selective force operating independently on movement and body size and generating the strongest selection against large, high‐velocity paramecia. Our results illustrate how ecology and genetics can shape potential natural selection on prey traits through the outcomes of trophic interactions. Further simultaneous measures of predation outcomes, traits, and their quantitative genetics will provide insights into the evolutionary ecology of species interactions and their eco‐evolutionary consequences. Read the free Plain Language Summary for this article on the Journal blog.

Genes to specialized metabolites: accumulation of scopoletin, umbelliferone and their glycosides in natural populations of Arabidopsis thaliana

BackgroundScopoletin and umbelliferone belong to coumarins, which are plant specialized metabolites with potent and wide biological activities, the accumulation of which is induced by various environmental stresses. Coumarins have been detected in various plant species, including medicinal plants and the model organism Arabidopsis thaliana. In recent years, key role of coumarins in maintaining iron (Fe) homeostasis in plants has been demonstrated, as well as their significant impact on the rhizosphere microbiome through exudates secreted into the soil environment. Several mechanisms underlying these processes require clarification. Previously, we demonstrated that Arabidopsis is an excellent model for studying genetic variation and molecular basis of coumarin accumulation in plants.ResultsHere, through targeted metabolic profiling and gene expression analysis, the gene-metabolite network of scopoletin and umbelliferone accumulation was examined in more detail in selected Arabidopsis accessions (Col-0, Est-1, Tsu-1) undergoing different culture conditions and characterized by variation in coumarin content. The highest accumulation of coumarins was detected in roots grown in vitro liquid culture. The expression of 10 phenylpropanoid genes (4CL1, 4CL2, 4CL3, CCoAOMT1, C3’H, HCT, F6’H1, F6’H2,CCR1 and CCR2) was assessed by qPCR in three genetic backgrounds, cultured in vitro and in soil, and in two types of tissues (leaves and roots). We not only detected the expected variability in gene expression and coumarin accumulation among Arabidopsis accessions, but also found interesting polymorphisms in the coding sequences of the selected genes through in silico analysis and resequencing.ConclusionsTo the best of our knowledge, this is the first study comparing accumulation of simple coumarins and expression of phenylpropanoid-related genes in Arabidopsis accessions grown in soil and in liquid cultures. The large variations we detected in the content of coumarins and gene expression are genetically determined, but also tissue and culture dependent. It is particularly important considering that growing plants in liquid media is a widely used technology that provides a large amount of root tissue suitable for metabolomics. Research on differential accumulation of coumarins and related gene expression will be useful in future studies aimed at better understanding the physiological role of coumarins in roots and the surrounding environments.

Beyond population size: whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.

Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of thirteen individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e., Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.

The impacts of positive selection on genomic variation in Drosophila serrata: Insights from a deep learning approach.

This study explores the impact of positive selection on the genetic composition of a Drosophila serrata population in eastern Australia through a comprehensive analysis of 110 whole genome sequences. Utilizing an advanced deep learning algorithm (partialS/HIC) and a range of inferred demographic histories, we identified that approximately 14% of the genome is directly affected by sweeps, with soft sweeps being more prevalent (10.6%) than hard sweeps (2.1%), and partial sweeps being uncommon (1.3%). The algorithm demonstrated robustness to demographic assumptions in classifying complete sweeps but faced challenges in distinguishing neutral regions from partial sweeps and linked regions under demographic misspecification. The findings reveal the indirect influence of sweeps on nearly two-thirds of the genome through linkage, with an over-representation of putatively deleterious variants suggesting that positive selection drags deleterious variants to higher frequency due to hitchhiking with beneficial loci. Gene ontology enrichment analysis further supported our confidence in the accuracy of sweep detection as several traits expected to be under positive selection due to evolutionary arms races (e.g. immunity) were detected in hard sweeps. This study provides valuable insights into the direct and indirect contributions of positive selection in shaping genomic variation in natural populations.

Heavy Metal Contamination in Birds from Protected Regions in the Amazon.

The extraction of crude oil and gold has substantially increased heavy metal contamination in the environment, yet the study of wildlife exposure and biological response to this pollution remains nascent even in the most biodiverse places in the world. We present a survey of heavy metal exposure in the feathers of wedge-billed woodcreepers (Glyphorynchus spirurus), a resident neotropical bird found within protected regions of the Amazon near oil and gold extraction sites. Our results show elevated heavy metal contamination in samples collected from protected areas proximate to known oil and gold extraction. Surprisingly, several samples from remote reference sites also displayed elevated levels of various heavy metals, suggesting a background of natural deposition or complex heavy metal contamination in the environment from anthropogenic sources. These results highlight the need to understand the ecological and biological impacts of increased heavy metal exposure on wildlife across space and time, including remote regions of the world purportedly untouched by these human-mediated stressors. Toward this goal, historical and contemporary data from native bird populations may provide crucial indicators for heavy metal contamination and exposure in wildlife and human communities. Environ Toxicol Chem 2024;00:1-7. © 2024 The Author(s). Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

Disparate and parallel craniofacial climatic adaptations in native populations of Asia, North America, and South America.

Understanding the impact that climate had in shaping cranial variation is critical for inferring the evolutionary mechanisms that played a role in human diversification. Here, we provide a comprehensive study aiming to analyze the association between climate and cranial variation of high latitude populations living in temperate to cold environments of Asia, North America, and South America. For this, we compiled a large morphometric dataset (N = 2633), which was combined with climatic and genomic data. We tested the influence of climate on the facial skeleton, nasal protrusion, and cranial vault and through multiple statistical tests at two geographical scales: intracontinental and intercontinental. We show that populations living in cold areas share a morphological pattern characterized by an increase in nasal height, facial and orbital heights and widths, a decrease in facial protrusion, and larger, longer, and lower cranial vaults. There are also distinctive features; populations from north Asia present the tallest noses, largest faces, and cranial vaults of the whole sample. Nasal breadth dimensions show small values in Asians, large values in South Americans, and non-significant changes in arctic North America. The morphological pattern in populations living at high latitude may be the result of parallel adaptation, as supported by physiological, morphometric, ecological, and genetic explanations, while the differences in magnitude and phenotypic expression could be due to the diverse population histories, severity of climate, and cultural strategies. Overall, our study shows that climate is a relevant factor shaping modern human morphology and it should be considered when studying modern human evolution and diversification.

Concomitant Serological and Molecular Methods for Strongyloides stercoralis Screening in an Endemic Area of Spain.

Strongyloidiasis is a widespread parasitic disease that can be life-threatening in immunosuppressed people. In the Mediterranean basin, autochthonous cases coexist with imported ones. We aimed to assess the utility of different screening methods, along with the frequency of strongyloidiasis and its associated risk factors in migrants and the native population. This cross-sectional study took place from 2019 to 2022 in the area of the Vega Baja Hospital in Alicante, Spain. Screening was performed in people who were immunosuppressed, at risk of immunosuppression, with blood asymptomatic eosinophilia, and in asymptomatic people from highly endemic countries. Screening methods were serological techniques (ELISA), stool parasitological tests (fecal concentration methods and agar plate culture), and a stool molecular test (PCR). Of the 168 participants (62.5% males, 53.0% migrants, 36.3% immunosuppressed, median age 57 years), 14 (8.3%) had confirmed strongyloidiasis, where 6 were confirmed by serology, 4 by PCR, and 4 by both methods. Overall, 9% of the migrants and 7.6% of the native-born patients were infected. Elevated IgE and hemoglobin and Latin American origin were associated with strongyloidiasis diagnosis. Screening with serology alone would have missed 28.6% of cases. We conclude that strongyloidiasis prevalence is high in our population, both in native and migrant groups, and stool PCR is a useful tool to increase case detection.

Floral dimorphism of Elsholtzia angustifolia (Loes.) Kitag. (Lamiaceae)

Gynodioecy is a sexual system in which hermaphrodites coexist with females and is frequently observed in Lamiaceae. The aim of this study was to investigate the floral morphology of Elsholtzia angustifolia (Loes.) Kitag (Lamiaceae) using stereomicroscopy (SM), light microscopy (LM), and scanning electron microscopy (SEM) to identify floral dimorphism in a potential gynodioecious species. Two different floral morphs were found in Elsholtzia angustifolia, hermaphroditic and female individuals, from three natural populations in South Korea (Ihwa Pass, Mt. Joryeong, and Mt. Sokli). However, females rarely occur in natural populations. Statistical analysis revealed significant size differences in the floral organs of the floral morphs. Micromorphological and anatomical characteristics were also examined using LM and SEM to compare the differences between the female and hermaphroditic types, revealing significant differences in the stamens between the two sexual types. Additionally, floral scent analysis was performed to identify floral morph-specific scent components, with elsholtzia ketone and dehydroelsholtzia ketone as the major components.

Semaglutide: An emerging treatment option for patients with obesity related HFpEF.

Dear Madam, Heart failure is a key contributor to patient morbidity and mortality and affects a staggering 64 million individuals around the globe1. An important sub-phenotype of heart failure is HFpEF, which is characterised by a left ventricular ejection fraction (LVEF) of 50 per-cent. Alarmingly, the incidence of this subtype has been rising globally, making the need for new treatment options extremely crucial2. Initially, the use of Semaglutide, a glucagon-like peptide-1 receptor agonist, showed favourable outcomes in cardiac function of mice. This study observed that weight loss achieved using Semaglutide was met with improvements in several factors associated with HFpEF (reduced LV hypertrophy and fibrosis, improved diastolic function, reduced lung congestion and improved exercise capacity) as compared to weight loss achieved through simple dietary means3. A step further in this direction is a clinical trial that shows that a weekly dosage of 2.4mg of Semaglutide in obesity related HFpEF patients is associated with significantly reduced symptoms and physical limitations, improved exercise function and greater weight loss than placebo4. Of the several parameters observed, improvements in CSS (Clinical Survey Score) of KCCQ (Kansas City Cardiomyopathy Questionnaire) and six minute walking distance were the most clinically meaningful. These promising findings are of particular value to Pakistani population, which has been prey to obesity and HF owing to Westernised eating habits, sedentary lifestyles and fewer healthcare facilities. In addition, South Asians have more fat content per BMI as compared to their white counterparts which coupled with the rising trends in NCD risks in South Asia5, are an immediate call for innovation in therapeutics. Semaglutide, considering its array of cardiometabolic benefits, may provide our doctors with a chance to step away from prescribing long lists of medications that are conventionally given to HF patients for symptom improvement. In a low- income country like Pakistan, this will ensure a better drug compliance and reduced disease burden. It is high time that we tap into the potential of Semaglutide and test its efficacy of it in our native population and take strides in ensuring its easy availability.

Responses of the mesozooplankton community to marine heatwaves: Challenges and solutions based on a long-term time series.

Marine heatwaves (MHWs) are extreme weather events that have major impacts on the structure and functioning of marine ecosystems worldwide. Due to anthropogenic climate change, the occurrence of MHWs is predicted to increase in future. There is already evidence linking MHWs with reductions in biodiversity and incidence of mass mortality events in coastal ecosystems. However, because MHWs are unpredictable, the quantification of their effects on communities is challenging. Here, we use the Helgoland Roads long-term time series (German Bight, North Sea), one of the richest marine time series in the world, and implement a modified before-after control-impact (BACI) design to evaluate MHW effect on mesozooplankton communities. Mesozooplankton play an essential role in connecting primary producers to higher trophic levels, and any changes in their community structure could have far-reaching impacts on the entire ecosystem. The responses of mesozooplankton community to MHWs in terms of community structure and densities occurred mainly in spring and autumn. Abundances of seven taxa, including some of the most abundant groups (e.g. copepods), were affected either positively or negatively in response to MHWs. In contrast, we observed no clear evidence of an impact of summer and winter MHWs; instead, the density of the most common taxa remained unchanged. Our results highlight the seasonally dependent impacts of MHWs on mesozooplankton communities and the challenges in evaluating those impacts. Long-term monitoring is an important contributor to the quantification of effects of MHWs on natural populations.

Population Characteristics and Habitat Management of the Useful Seaweed Silvetia siliquosa

We aimed to analyze the natural population characteristics and habitat growth conditions of the valuable seaweed Silvetia siliquosa. Its population characteristics and habitat conditions were assessed monthly from May 2022 to April 2023 and April to August 2022, respectively, on selected habitats. The average population density, coverage, and frequency of S. siliquosa were 579 ± 94.18 ind./m2, 27.82 ± 6.92%/m2, and 78.37 ± 5.98/m2, respectively. The average thallus length and width were 47.53 ± 4.35 and 46.33 ± 4.17 mm, respectively, while the branch width, thickness, and frequency were 2.35 ± 0.03 mm, 0.59 ± 0.12 mm, and 2.8 ± 0.2 times, with a receptacle length and width of 24.13 ± 2.07 and 2.81 ± 0.19 mm, respectively. Among the 40 previously known natural habitats of S. siliquosa, growth was confirmed only in Sepo, Sebang, and Bangpo. The causes for the declining S. siliquosa populations could be attributed to habitat changes due to construction, coastal road maintenance projects, habitat disturbances, and increased pollutants. Habitat substrate disturbances and changes were the main causes of the decrease in S. siliquosa growth. Studies on environmental factors and habitat degradation, growth related to environmental factors, mass cultivation, and the marine ecosystem restoration of S. siliquosa are needed.

Insertions and Deletions: Computational Methods, Evolutionary Dynamics, and Biological Applications.

Insertions and deletions constitute the second most important source of natural genomic variation. Insertions and deletions make up to 25% of genomic variants in humans and are involved in complex evolutionary processes including genomic rearrangements, adaptation, and speciation. Recent advances in long-read sequencing technologies allow detailed inference of insertions and deletion variation in species and populations. Yet, despite their importance, evolutionary studies have traditionally ignored or mishandled insertions and deletions due to a lack of comprehensive methodologies and statistical models of insertions and deletion dynamics. Here, we discuss methods for describing insertions and deletion variation and modeling insertions and deletions over evolutionary time. We provide practical advice for tackling insertions and deletions in genomic sequences and illustrate our discussion with examples of insertions and deletion-induced effects in human and other natural populations and their contribution to evolutionary processes. We outline promising directions for future developments in statistical methodologies that would allow researchers to analyze insertions and deletion variation and their effects in large genomic data sets and to incorporate insertions and deletions in evolutionary inference.

Integrating RTM-GWAS and meta‑QTL data revealed genomic regions and candidate genes associated with the first fruit branch node and its height in upland cotton.

Two genomic regions associated with FFBN and HFFBN and a potential regulatory gene (GhE6) of HFFBN were identified through the integration of RTM-GWAS and meta‑QTL analyses. Abstract The first fruit branch node (FFBN) and the height of the first fruit branch node (HFFBN) are two important traits that are related to plant architecture and early maturation in upland cotton. Several studies have been conducted to elucidate the genetic basis of these traits in cotton using biparental and natural populations. In this study, by using 9,244 SNP linkage disequilibrium block (SNPLDB) loci from 315 upland cotton accessions, we carried out restricted two-stage multilocus and multiallele genome-wide association studies (RTM-GWASs) and identified promising haplotypes/alleles of the four stable and true major SNPLDB loci that were significantly associated with FFBN and HFFBN. Additionally, a meta-quantitative trait locus (MQTL) analysis was conducted on 274 original QTLs that were reported in 27 studies, and 40 MQTLs associated with FFBN and HFFBN were identified. Through the integration of the RTM-GWAS and meta‑QTL analyses, two stable and true major SNPLDBs (LDB_5_15144433 and LDB_16_37952328) that were distributed in the two MQTLs were identified. Ultimately, 142 genes in the two genomic regions were annotated, and three candidate genes associated with FFBN and HFFBN were identified in the genomic region (A05:14.64-15.64Mb) via RNA-Seq and qRT‒PCR. The results of virus-induced gene silencing (VIGS) experiments indicated that GhE6 was a key gene related to HFFBN and that GhDRM1 and GhGES were important genes associated with early flowering in upland cotton. These findings will aid in the future identification of molecular markers and genetic resources for developing elite early-maturing cultivars with ideal plant characteristics.

Viewing Native American Cervical Cancer Disparities through the Lens of the Vaginal Microbiome: A Pilot Study.

Vaginal dysbiosis is implicated in persistent HPV infection and cervical cancer. Yet, there is a paucity of data on the vaginal microbiome in Native American communities. Here, we aimed to elucidate the relationships between microbiome, HPV, sociodemographic and behavioral risk factors to better understand an increased cervical cancer risk in Native American women. In this pilot study, we recruited 31 participants (16 Native American, 15 non-Native women) in Northern Arizona and examined vaginal microbiota composition, HPV status, and immune mediators. We also assessed individuals' sociodemographic information, and physical, mental, sexual, and reproductive health. Overall, microbiota profiles were dominated by common Lactobacillus species (associated with vaginal health) or a mixture of bacterial vaginosis-associated bacteria. Only 44% of Native women exhibited Lactobacillus dominance, compared to 58% of non-Native women. Women with vaginal dysbiosis also had elevated vaginal pH and were more frequently infected with high-risk HPV. Furthermore, we observed associations of multiple people in a household, lower level of education, and high parity with vaginal dysbiosis and abundance of specific bacterial species. Finally, women with dysbiotic microbiota presented with elevated vaginal levels of proinflammatory cytokines. Altogether, these findings indicate an interplay between HPV, vaginal microbiota, and host defense, which may play a role in the cervical cancer disparity among Native American women. Future longitudinal studies are needed to determine the mechanistic role of vaginal microbiota in HPV persistence in the context of social determinants of health toward the long-term goal of reducing health disparities between non-Hispanic White and Native American populations.

Attitudes and prejudice towards immigration in rural and urban contexts in Spain

Introduction: For years now, Spain has been a country that receives immigration wherein different cultures coexist. The aim of this research is to examine the levels of attitudes, subtle and blatant prejudice, as well as their dimensions, from native people to immigrant people in urban and rural areas. Methodology: The scale adapted to the native population by Rueda and Navas is from Meertens and Pettigrew’s scales of subtle and blatant prejudice and the scale of attitudes towards immigration by León, Mira & Gómez. Results: The results obtained from the prejudice scale (α=.804) and attitudes scale (α=.672) demonstrate an appropriate level of internal consistency. Results reveal that people living in rural areas did not exhibit higher levels of prejudice (subtle and blatant) than people living in urban areas. Discussion: Furthermore, people living in rural areas did not exhibit higher levels of attitudes (equality principles and policies attitude) than people living in urban areas. Conclusions: Finally, people living in rural areas did not exhibit higher levels of attitudes (negative social distancing attitude) than people living in urban areas. The results obtained are discussed, referring to the previous literature.

Circadian and environmental signal integration in a natural population of Arabidopsis

Plants sense and respond to environmental cues during 24 h fluctuations in their environment. This requires the integration of internal cues such as circadian timing with environmental cues such as light and temperature to elicit cellular responses through signal transduction. However, the integration and transduction of circadian and environmental signals by plants growing in natural environments remains poorly understood. To gain insights into 24 h dynamics of environmental signaling in nature, we performed a field study of signal transduction from the nucleus to chloroplasts in a natural population of Arabidopsis halleri. Using several modeling approaches to interpret the data, we identified that the circadian clock and temperature are key regulators of this pathway under natural conditions. We identified potential time-delay steps between pathway components, and diel fluctuations in the response of the pathway to temperature cues that are reminiscent of the process of circadian gating. We found that our modeling framework can be extended to other signaling pathways that undergo diel oscillations and respond to environmental cues. This approach of combining studies of gene expression in the field with modeling allowed us to identify the dynamic integration and transduction of environmental cues, in plant cells, under naturally fluctuating diel cycles.

Andean Lakes: endangered by natural and anthropogenic threats

The Andes mountains extend North-South in a latitudinal gradient of 8,500 km. Due to the great climatic variety and the peculiar north-south orographic distribution, lakes are very diverse, including different lake origins and very contrasting morphometries. Here, we reviewed more than 700 ecological studies on Andean lakes to identify the main threats to these freshwater systems. The most important threats are UV radiation, changes in water balance, eutrophication, all three interacting with climate change, alien species introduction, and mining. Ultraviolet radiation is an important factor in Andean lakes not only because of the altitude but also because many lakes are included in the Antarctic ozone hole. The introduction of alien species, particularly exotic salmonids, also had detrimental effects, affecting native fish populations and behaviour, and endemic species by disrupting the indigenous food web. Eutrophication and browning caused by human activities, including land use interacting with climate change, are increasing in Andean lakes causing a decrease in water quality. Finally, mining can cause water contamination (both groundwater and surface water) by chemicals emitted from mining processes thus, producing a loss of biodiversity. Although an important number of Andean lakes have been declared as RAMSAR sites because of their uniqueness and their extreme conditions, they are subject to significant human impacts. Here, for the first time, we identify these impacts all along the Andes, however, further studies at different scales are mandatory if we pretend to understand, conserve, and manage Andean lakes.

Unveiling population structure and selection signatures of riverine and genetically improved rohu, Labeo rohita using genome wide SNPs.

Captive breeding, along with artificial selection can significantly impact population structure by influencing allele frequencies and driving populations towards specific adaptation. Selective sweeps are powerful forces in shaping genetic variation within populations and can drive rapid spread of beneficial alleles while simultaneously reducing genetic diversity in localized regions of the genome. The present work was undertaken to assess the genetic structure and consequences of artificial selection in 10th generation of genetically improved rohu by comparing with wild populations. The present study used 11,022 high-quality genome wide SNPs to compare the population genetic structure and signatures of selection between Jayanti rohu population and its wild counterpart. Outlier analysis revealed presence of 14 adaptive SNPs, out of which 5 were classified to be under decisive selection pressure. Notably, Jayanti rohu (JR) displayed 297 private alleles exclusive to its population. Chromosomes 7 and 16 emerged as potential hotspots containing a majority of the identified SNPs. Structure and principal component analysis revealed two distinct clusters, effectively distinguishing the JR and wild rohu populations. Phylogenetic analysis indicated a separate cluster of JR population distant from wild groups. The results of present study shall help in elucidating patterns of genetic variation and characterizing selection signatures associated with captive bred and natural populations of rohu. The genomic resources generated through this work shall be helpful in improving the traceability of selectively bred germplasm for developing future strategies of genetic management.

Identification of body coloration related genes in ricefield eel (Monopterus albus) using GWAS

Body color is one of the most diverse external morphological characteristics of fish. It not only affects the function of fish predation and individual communication but also has important economic value. The ricefield eel (Monopterus albus) is a popular freshwater aquaculture fish species in China. Few studies have suggested some candidate genes involved in the formation of body color in this fish; however, further genetic evidences are required. Genome-wide association analysis (GWAS) is a powerful analytical method for identifying relationships between target traits and genetic markers or candidate genes in natural populations. In this study, two populations of ricefield eel with different body coloration were used to study the genetic factors that regulate the formation of body color. Through GWAS, 67 SNPs, 463 genes and 5 signaling pathways were found to be associated with body color. These results suggest that a complex molecular regulatory mechanism regulates ricefield eel body coloration. Our findings lay the foundation for subsequent genome selection breeding of ricefield eel.