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Human population growth constantly requires an increase in the production of food and products from the timber industry. To meet this demand, agriculture and planted forests are advancing over natural areas. In view of this, it is necessary to know the effects of land use for different purposes (grain production, pastures, planted forests, fruit production and among other uses) on the genetic diversity of populations of native species. This knowledge can assist in land use planning as well as in the development of conservation strategies for native species. In this study, we evaluated the effect of land use for agriculture (mainly for cereal production) and planted forests on the genetic diversity of Baccharis crispa Spreng., a herb native to South America. To achieve our goals, we compared population genetic data obtained with three molecular markers (microsatellites, inter-simple sequence repeat and isoenzymes) with data on land use for agriculture and planted forests from 15 different locations. Our results showed that regardless of the molecular marker used, the greater the use of land for agriculture and planted forests, the lower was the genetic diversity of B. crispa populations. Baccharis crispa is a semi-perennial species that needs at least one year to reach its reproductive period, which is prevented in agricultural areas due to the land being turned over or dissected with herbicides every 6 months. In the studied regions, the planted forests are of eucalypt and/or pine, which besides being species with a high production of allelopathic substances, produce strong shading and B. crispa is a species that inhabits open grassland that needs a high incidence of sunlight for development. The data obtained in our study can assist in the decision-making to use land in order to reconcile the production of supplies for humanity and for the conservation of nature.

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Arboreal ants are ecologically important in tropical forests, but there are few studies using DNA markers to examine their population and colony structure. Colonies of the arboreal turtle ant Cephalotes goniodontus create trail networks through the canopy of the tropical forest, in dense vegetation where it is difficult to determine how long a nest is used and how neighboring colonies partition space. We monitored 53 nest sites for up to six years and, using seven microsatellite markers, genotyped samples of workers collected at or near 41 nests over 1-4 years. We calculated average relatedness within samples collected at a given location, and between samples collected at the same location in successive years, and performed pedigree analysis to predict the number of queens that produced each sample of workers. Fifteen samples were highly related (r ≥ 0.6) from single colonies, of which 11 were monogynous and the remaining four had two queens; 19 were of intermediate relatedness (0.1 ≤ r < 0.6) with 1-6 queens, and 7 were groups of unrelated workers (r < 0.1) from at least 4 queens. Colonies persisted at the same nest site for 2-6 years. The smallest distance we found separating nests of different colonies was 16.2 m. It appears that different colonies may share foraging trails. Our study demonstrates the feasibility of using a cost-efficient genotyping method to provide information on colony structure and life history of ant species. Supplementary Information: The online version contains supplementary material available at 10.1007/s00040-024-00974-3.

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Glacial periods have been considered as inhospitable environments that consist of treeless vegetation at higher latitudes. The fossil record suggests many species survived the Last Glacial Maximum within refugia, usually at lower latitudes. However, phylogeographic studies have given support to the existence of previously unknown high-latitude refugia that were not detected in the fossil record. Here, we test the hypothesis that cold-tolerant trees of Patagonia survived cold periods in microclimatically favourable locales where hybridization occurred between sister taxa. To study local presence through glacial periods in multiple refugia, we used pollen records and genetic information (isozymes, microsatellites, and combined nuclear and chloroplast DNA sequences) of population pairs of Nothofagus antarctica and N. pumilio that belong to the ancient subgenus Nothofagus which can potentially hybridize in nature, along their entire latitudinal range in Patagonia. Studied species share the N. dombeyi type pollen, which was abundant at >20% in the northernmost latitudinal bands (35-43°S), even during the Last Glacial Maximum. Mid- and southern latitudinal records (44-55°S) yielded lower abundances of ~10% that increased after c. 15.0 cal. ka BP. Therefore, fossil pollen evidence suggests a long-lasting local presence of Nothofagus throughout glacial-interglacial cycles but mostly as small populations between 44°S and 51°S. We found species-specific and shared genetic variants, the latter of which attained relatively high frequencies, thus providing evidence of ancestral polymorphisms. Populations of each species were similarly diverse, suggesting survival throughout the latitudinal range. Estimates of coalescent divergence times were broadly synchronous across latitudes, suggesting that regional climates similarly affected populations and species that hybridized through climate cycles, fostering local persistence.

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The pink river dolphin, or bufeo, is one of the dolphins which lives in the rivers of the Orinoco and Amazon basins in South America. The Bolivian bufeo population is considered a differentiated species (Inia boliviensis) from the Amazon and Orinoco species (Inia geoffrensis). Until now, no study has completed an extensive population genetics analysis of the bufeo in Bolivian rivers. We analyzed 82 bufeos from different rivers from the Mamoré and Iténez (Guaporé) river basins for the mt control region (CR), nuclear microsatellites, and DQB-1 gene sequences to determine if the inner rapids of these Bolivian river basins have some influence on the genetic structure of this species. The first relevant result was that the genetic diversity for CR, and the microsatellites were substantially lower in the Bolivian bufeos than in the dolphins studied in other areas of the Amazon and Orinoco. However, the DQB-1 gene sequences yielded similar genetic diversity to those found in other areas. The second relevant result is the existence of some significant genetic heterogeneity among the bufeo populations within Bolivia, although in a small degree, but this differentiation is independent of the inner rapids of the Bolivian rivers we sampled. The third relevant result was the existence of significant isolation by distance for the CR, but not for microsatellites and DQB-1 gene sequences. This was related to differential gene flow capacity of females (philopatric) and males (less philopatric and more migrants) and, possibly, to different selective patterns affecting the molecular markers studied. The fourth relevant result was related to diverse demographic changes of these bufeos. At least two or three bottleneck events and one or two population expansions have occurred in the Bolivian bufeo population. The major part of these events occurred during the Pleistocene.

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Environmental gradients in the sea may coincide with phenotypic or genetic gradients resulting from an evolutionary balance between selection and dispersal. The population differentiation of the swimming crab, Liocarcinus depurator, an important by-catch species in the Mediterranean Sea and North-East Atlantic, was assessed using both genetic and morphometric approaches. A total of 472 specimens were collected along its distribution area, and 17 morphometric landmarks, one mitochondrial gene (COI) and 11 polymorphic microsatellite markers were scored in 350, 287 and 280 individuals, respectively. Morphometric data lacked significant differences, but genetic analyses showed significant genetic differentiation between Atlantic and Mediterranean populations, with a steeper gradient in COI compared to microsatellite markers. Interestingly, nuclear differentiation was due to an outlier locus with a gradient in the Atlantic-Mediterranean transition area overlapping with the mtDNA gradient. Such overlapping clines are likely to be maintained by natural selection. Our results suggest a scenario of past isolation with local adaptation and secondary contact between the two basins. Local adaptation during the process of vicariance may reinforce genetic differentiation at loci maintained by environmental selection even after secondary contact.

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The Doradidae fishes constitute one of the most diverse groups of Neotropical freshwater environments. Acanthodoradinae is the oldest lineage and the sister group to all other thorny catfishes, and it includes only the genus Acanthodoras. The diversity of Acanthodoras remains underestimated, and the use of complementary approaches, including genetic studies, is an important step to better characterize this diversity and the relationships among the species within the genus. Therefore, we conducted a comprehensive analysis using conventional cytogenetic techniques and physical mapping of three multigene families (18S and 5S ribosomal DNA [rDNA], U2 small nuclear DNA [snDNA]) and four microsatellite motifs, namely (AC)n, (AT)n, (GA)n, and (GATA)n, in two sympatric species from the Negro River: Acanthodoras cataphractus and Acanthodoras cf. polygrammus. We found significant differences in constitutive heterochromatin (CH) content, distribution of the microsatellite (AT)n, and the number of 5S rDNA and U2 snDNA sites. These differences may result from chromosome rearrangements and repetitive DNA dispersal mechanisms. Furthermore, the characterization of the diploid number (2n) of these Acanthodoras species enables us to propose 2n = 58 chromosomes as the plesiomorphic 2n state in Doradidae based on ancestral state reconstruction. Acanthodoradinae is the oldest lineage of the thorny catfishes, and knowledge about its cytogenetic patterns is crucial for disentangling the karyotype evolution of the whole group. Thus, this study contributes to the understanding of the mechanisms behind chromosome diversification of Doradidae and highlights the importance of Acanthodoradinae in the evolutionary history of thorny catfishes.

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Trypanosoma cruzi, the causative agent of Chagas disease, is primarily transmitted to humans by hematophagous bugs of the Triatominae subfamily. In the Colombian Caribbean region, particularly on Margarita Island, T. cruzi transmission is highly endemic and associated with vectors such as Triatoma maculata and Rhodnius pallescens. Additionally, T. cruzi-infected Didelphis marsupialis are commonly found in close proximity to human dwellings. Given the complex transmission dynamics involving various domestic and non-domestic hosts, this study aimed to analyze 145 T. cruzi clones from twelve strains isolated from T. maculata, R. pallescens, and D. marsupialis using spliced leader intergenic region (SL-IR) sequences and nine polymorphic microsatellite loci. The results indicate the presence of a single polymorphic T. cruzi population, suggesting sustained local transmission dynamics between triatomines adapted to A. butyracea forests and peridomestic areas inhabited by synanthropic mammal reservoir such as D. marsupialis. Notably, this population appears to lack substructure, highlighting the importance of adopting an alternative eco-health approach to complement traditional chemical vector control methods for more effective and sustainable interruption of transmission.

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The high dynamism of repetitive DNAs is a major driver of chromosome evolution. In particular, the accumulation of repetitive DNA sequences has been reported as part of the differentiation of sex-specific chromosomes. In turn, the fish species of the genus Megaleporinus are a monophyletic clade in which the presence of differentiated ZZ/ZW sex chromosomes represents a synapomorphic condition, thus serving as a suitable model to evaluate the dynamic evolution of repetitive DNA classes. Therefore, transposable elements (TEs) and in tandem repeats were isolated and located on chromosomes of Megaleporinus obtusidens and M. reinhardti to infer their role in chromosome differentiation with emphasis on sex chromosome systems. Despite the conserved karyotype features of both species, the location of repetitive sequences - Rex 1, Rex 3, (TTAGGG)n, (GATA)n, (GA)n, (CA)n, and (A)n - varied both intra and interspecifically, being mainly accumulated in Z and W chromosomes. The physical mapping of repetitive sequences confirmed the remarkable dynamics of repetitive DNA classes on sex chromosomes that might have promoted chromosome diversification and reproductive isolation in Megaleporinus species.

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This study characterizes the chromosomal organization of DNA repetitive sequences and the karyotypic evolution in four representatives of the solitary wasp genus Trypoxylon using conventional and molecular cytogenetic techniques. Our findings present the first cytogenetic data for Trypoxylon rogenhoferi (2n = 30) and Trypoxylon albonigrum (2n = 32), while the karyotypes of Trypoxylon nitidum (2n = 30) and Trypoxylon lactitarse (2n = 30) were similar to those previously described. Fluorochrome staining and microsatellite distribution data revealed differences in the constitutive heterochromatin composition among species. Trypoxylon nitidum and T. albonigrum exhibited one major rDNA cluster, potentially representing an ancestral pattern for aculeate Hymenoptera, while T. rogenhoferi and T. lactitarse showed two pericentromeric rRNA gene sites, suggesting amplification events in their ancestral clade. The (TCAGG)n motif hybridized in the terminal regions of the chromosomes in all four Trypoxylon species, which may suggest that this sequence represents DNA telomeric repeat. Notably, the presence of this repetitive sequence in the centromeric regions of certain chromosome pairs in two species supports the hypothesis of chromosomal fusions or inversions in the ancestral karyotype of Trypoxylon. The study expands the chromosomal mapping data of repetitive sequences in wasps and offers insights into the dynamic evolutionary landscape of karyotypes in these insects.

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The hoary fox (Lycalopex vetulus) is the only species of the Canidae (Mammalia: Carnivora) endemic to Brazil, and so far has been the target of few genetic studies. Using microsatellites and mtDNA markers, we investigated its present genetic diversity and population structure. We also tested the hypothesis that this species currently hybridizes with the pampas fox (L. gymnocercus), as suggested by previous mtDNA data from two individuals. We collected tissue and blood samples from animals representing most of the two species' distributions in Brazil (n = 87), including their recently discovered geographic contact zone in São Paulo state. We observed that the hoary fox exhibits high levels of genetic diversity and low levels of population structure. We identified six individuals from São Paulo state with clear evidence of hybridization based on introgressed pampas fox mitochondrial DNA and/or admixed microsatellite genotypes (three individuals bore both types of evidence). These results demonstrate the existence of admixed individuals between hoary and pampas foxes in southeastern Brazil, representing the first identified case of interspecies admixture between native South American canids. We discuss our findings in the context of the evolutionary history of these foxes and address potential conservation implications of this interspecies hybridization process.

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The application of the sterile insect technique (SIT) requires the adaptation of insects to mass-rearing conditions. It is generally accepted that this adaptation may include a reduction in genetic diversity and an associated loss of desirable characteristics for the effective performance of sterile insects in the field. Here, we compare the genetic diversity of two mass-reared strains of the Mexican fruit fly, Anastrepha ludens, and a wild (WIL) population collected near Tapachula, Mexico, using seven DNA microsatellites as molecular genetic markers. The mass-reared strains were a bisexual laboratory strain (LAB) with approximately 130 generations under mass-rearing and a genetic sexing strain, Tapachula-7 (TA7), also under mass-rearing for 100 generations. Our results revealed an overall low level of genetic differentiation (approximately 15%) among the three strains, with the LAB and WIL populations being genetically most similar and TA7 most genetically differentiated. Although there were some differences in allele frequencies between strains, our results show that overall, the adaptation to mass-rearing conditions did not reduce genetic variability compared to the wild sample in terms of heterozygosity or allelic richness, nor did it appear to alter the level of inbreeding with respect to the wild populations. These results are contrary to the general idea that mass-rearing always results in a reduction in genetic diversity. Overall, our findings can contribute to a better understanding of the impact that adaptation to mass-rearing conditions may have on the genetic make-up of strains.

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Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria.

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Restricted movement among populations decreases genetic variation, which may be the case for the Montezuma quail (Cyrtonyx montezumae), a small game bird that rarely flies long distances. In the northern limit of its distribution, it inhabits oak-juniper-pine savannas of Arizona, New Mexico, and Texas. Understanding genetic structure can provide information about the demographic history of populations that is also important for conservation and management. The objective of this study was to determine patterns of genetic variation in Montezuma quail populations using nine DNA microsatellite loci. We genotyped 119 individuals from four study populations: Arizona, Western New Mexico, Central New Mexico, and West Texas. Compared to other quail, heterozygosity was low (H¯0 = 0.22 ± 0.04) and there were fewer alleles per locus (A = 2.41 ± 0.27). The global population genetic differentiation index RST = 0.045 suggests little genetic structure, even though a Bayesian allocation analysis suggested three genetic clusters (K = 3). This analysis also suggested admixture between clusters. Nevertheless, an isolation-by-distance analysis indicates a strong correlation (r = 0.937) and moderate evidence (P = 0.032) of non-independence between geographical and genetic distances. Climate change projections indicate an increase in aridity for this region, especially in temperate ecosystems where the species occurs. In this scenario, corridors between the populations may disappear, thus causing their complete isolation.

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The creole pigs represent 67% of the national population in Peru. They are a source of economic income in rural communities, and due to their rusticity, they are not much labor demanding. However, knowledge about its genetic diversity remains scarce. The objective of this study was to determine the population structure and genetic diversity of creole pigs from rural communities in south central Peru. Thirteen microsatellites were used to characterize 120 creole pigs from the departments of Ayacucho (57) and Apurimac (63). The samples were taken from hair follicles and ear tissue. Nine microsatellites were highly polymorphic and informative (PIC > 0.5) for both departments. The Ayacucho population had a mean number of alleles (MNA) and expected heterozygosity (HE) of 8.8 and 0.68, respectively, while in the Apurimac population, these were 8.9 and 0.71, respectively. Both populations showed in less than 50% of their loci a deviation from Hardy-Weinberg equilibrium. There was a moderate genetic structure according to the analysis of molecular variance and the FST statistics (0.06), which was corroborated by Bayesian methods. In conclusion, the genetic diversity was mostly due to the intrapopulation variance (91%). Some individuals from Ayacucho shared similar alleles with those from Apurimac. This latter result may be due to their geographic proximity and the introduction of the same new exotic breeds. This is the first research on the genetic diversity of creole pigs in south central Peru. In fact, this study could serve as a basis for conservation strategies and actions in this region.

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Varroa destructor is a damaging mite of Western honey bees (Apis mellifera). Genetic variability of the mite in different regions of the world could be related to the movement of infested bees or other factors, such as climate. In this study, V. destructor samples were collected from tropical and temperate climate regions of Mexico, and a humid continental climate region of Canada. COX-1 AFLPs showed that all the mites were the Korean haplotype. Four microsatellites revealed nine haplogroups from the continental climate region of Canada, compared to three haplogroups from the tropical and temperate climate regions of Mexico. CytII-ATP sequences showed seven haplogroups from the humid continental climate region vs. two haplogroups from the temperate region and one haplogroup from the tropical region. CytB sequences revealed seven haplogroups from Canada vs. three from Mexico. A comparison of the cytB sequences of the samples from Canada and Mexico to those from a worldwide collection showed that one sequence, designated the cytB1 type, predominated, comprising 57% of the 86 sequences; it clustered with similar sequences that comprised 80% of the sequences, designated family A. CytB1 was predominant in Mexico, but not in Canada. The other 20% of sequences were in families B and C, and all those samples originated from East and Southeast Asia. The microsatellite, cytII-ATP, and cytB markers, all showed higher variability in mites collected in Canada than in Mexico, which could be related to the cooler climate or an earlier invasion and/or multiple mite invasions in Canada.

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Microsatellites, also known as SSRs or STRs, are polymorphic DNA regions with tandem repetitions of a nucleotide motif of size 1-6 base pairs with a broad range of applications in many fields, such as comparative genomics, molecular biology, and forensics. However, the majority of researchers do not have computational training and struggle while running command-line tools or very limited web tools for their SSR research, spending a considerable amount of time learning how to execute the software and conducting the post-processing data tabulation in other tools or manually-time that could be used directly in data analysis. We present EasySSR, a user-friendly web tool with command-line full functionality, designed for practical use in batch identifying and comparing SSRs in sequences, draft, or complete genomes, not requiring previous bioinformatic skills to run. EasySSR requires only a FASTA and an optional GENBANK file of one or more genomes to identify and compare STRs. The tool can automatically analyze and compare SSRs in whole genomes, convert GenBank to PTT files, identify perfect and imperfect SSRs and coding and non-coding regions, compare their frequencies, abundancy, motifs, flanking sequences, and iterations, producing many outputs ready for download such as PTT files, interactive charts, and Excel tables, giving the user the data ready for further analysis in minutes. EasySSR was implemented as a web application, which can be executed from any browser and is available for free at https://computationalbiology.ufpa.br/easyssr/. Tutorials, usage notes, and download links to the source code can be found at https://github.com/engbiopct/EasySSR.

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Genetic and morphological structure of vector populations are useful to identify panmictic groups, reinfestation sources and minimal units for control interventions. Currently, no studies have integrated genetic and morphometric data in Triatoma infestans (Hemiptera: Reduviidae), one of the main vectors of Trypanosoma cruzi. We characterized the genetic and phenotypic structure of T. infestans at a small spatial scale (2-8 km), identified potential migrants and compared flight-related traits among genetic groups and between migrant and non-migrant insects in a well-defined area without insecticide spraying in the previous 12 years. We obtained microsatellite genotypes (N = 303), wing shape and size (N = 164) and body weight-to-length ratios (N = 188) in T. infestans from 11 houses in Pampa del Indio, Argentine Chaco. The uppermost level of genetic structuring partially agreed with the morphological groups, showing high degrees of substructuring. The genetic structure showed a clear spatial pattern around Route 3 and one genetic group overlapped with an area of persistent infestation and insecticide resistance. Females harboured more microsatellite alleles than males, which showed signs of isolation-by-distance. Wing shape discriminant analyses of genetic groups revealed low reclassification scores whereas wing size differed among genetic groups for both sexes. Potential migrants (8%) did not differ from non-migrants in sex, ecotope, wing shape and size. However, male migrants had lower W/L than non-migrants suggesting poorer nutritional state. Our findings may contribute to the understanding of population characteristics, dispersal dynamics and ongoing elimination efforts of T. infestans.

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This study focused on analyzing the distribution of microsatellites in holocentric chromosomes of the Triatominae subfamily, insect vectors of Chagas disease. We employed a non-denaturing FISH technique to determine the chromosomal distribution of sixteen microsatellites across twenty-five triatomine species, involving five genera from the two principal tribes: Triatomini and Rhodniini. Three main hybridization patterns were identified: strong signals in specific chromosomal regions, dispersed signals dependent on microsatellite abundance and the absence of signals in certain chromosomal regions or entire chromosomes. Significant variations in hybridization patterns were observed between Rhodniini and Triatomini species. Rhodniini species displayed weak and scattered hybridization signals, indicating a low abundance of microsatellites in their genomes. In contrast, Triatomini species exhibited diverse and abundant hybridization patterns, suggesting that microsatellites are a significant repetitive component in their genomes. One particularly interesting finding was the high abundance of GATA repeats, and to a lesser extent AG repeats, in the Y chromosome of all analyzed Triatomini species. In contrast, the Y chromosome of Rhodniini species did not show enrichment in GATA and AG repeats. This suggests that the richness of GATA repeats on the Y chromosome likely represents an ancestral trait specific to the Triatomini tribe. Furthermore, this information can be used to elucidate the evolutionary relationships between Triatomini and other groups of reduviids, contributing to the understanding of the subfamily's origin. Overall, this study provides a comprehensive understanding of the composition and distribution of microsatellites within Triatominae genomes, shedding light on their significance in the evolutionary processes of these species.

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Centropomus undecimalis (common snook) and Centropomus parallelus (fat snook) have a wide distribution from southern Florida to southern Brazil. Due to their value as a food source, these species have been heavily exploited through predatory fishing, posing a conservation challenge. To assess their genetic diversity and population structure, we used microsatellite markers. Our findings revealed genetic differences among populations of the same species, highlighting the need for targeted conservation efforts. The microsatellite markers proved effective in assessing genetic variability, providing valuable insights for management and conservation. The parameters Ho (observed heterozygosity) and He (expected heterozygosity) were reliable indicators of genetic diversity, and specific loci showed varying allele numbers across populations. Our study contributes to understanding population genetics in these snook species and supports their conservation. Despite not being classified as endangered, genetic differences among populations emphasize the importance of considering population-level characteristics in conservation strategies. This research lays the foundation for future studies and actions aimed at preserving these valuable fish species. In summary, our study demonstrates the significance of microsatellite markers in assessing genetic variability and population structure in common snook and fat snook, informing conservation efforts for these species.

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Background: Semaprochilodus insignis is a migratory fish of commercial and subsistence importance to communities in the Amazon. Despite the high intensity of exploitation, recent studies have not been carried out to assess the genetic status of its stocks. Methods: This study is the first to estimate genetic diversity and to test the existence of spatial and temporal structuring of S. insignis through sequencing of the mtDNA control region (n = 241) and eight microsatellite loci (n = 180) of individuals sampled at 11 sites distributed in the Brazilian Amazon basin. Results: Results for both markers were congruent, revealing a homogeneous genetic diversity in all the sampled locations, in addition to the absence of spatial and temporal genetic structure, indicating that the species forms a large panmictic population in the Brazilian Amazon. Discussion: Although overfishing does not yet appear to have affected the levels of genetic variability of S. insignis, signals of reduction of the effective population size and a bottleneck provide an early alert to the effects of overfishing. Thus, the ever-decreasing populations may threaten S. insignis in the future. Therefore, it is hoped that the results of this study may contribute to the elaboration of management plans or any other measures that aim at the management and conservation of this species of great importance for the Amazon basin.

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