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In paternity testing, DNA polymorphism analysis not only settles explicitly disputed paternity issue but also provides information on mutation frequencies in STR loci. In this study, insertion or deletion of one repetitive unit was observed in 38 of 32,391 meiotic transfers analysed in 953 paternity testing cases. Parentage samples from Upper Silesia (southern Poland) were examined in 2008–2014 with the use of three commercially available amplification kits: AmpFlSTR Identifiler (Applied Biosystems), PowerPlex 16 HS (Promega) and PowerPlex ESX 17 (Promega). The rate of paternal mutations was 4.6 times higher than that of maternal ones. The highest mutation rate was noted at VWA locus. Interpopulation comparisons showed statistically significant differences in mutation rates of several STRs between Upper Silesia and populations from Brazil and China. There were no differences in occurrence of mutations between a population from Upper Silesia and another southern Polish population from a region of Lesser Poland. Our results suggest that knowledge of STR mutation rates in different populations may be important for calculations of probability of relationship in disputed paternity testing and that such calculations should be based on population-specific mutation rates, at least for some STR markers used commonly in forensic genetics. [ABSTRACT FROM AUTHOR]

Copyright of Animal Biodiversity & Conservation is the property of Museu de Ciencies Naturals de Barcelona and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: = 0.211 and S. spontaneum: = 0.216, P<0.001), and significant contribution of the latter in the genetic variability of commercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny. [ABSTRACT FROM AUTHOR]

Sotalia guianensis is a small dolphin that is vulnerable to anthropogenic impacts. Along the Brazilian Atlantic coast, this species is threatened with extinction. A prioritized action plan for conservation strategies relies on increased knowledge of the population. The scarcity of studies about genetic diversity and assessments of population structure for this animal have precluded effective action in the region. Here, we assessed, for the first time, the genetic differentiation at 14 microsatellite loci in 90 S. guianensis specimens stranded on the southeastern Atlantic coast of the State of Espírito Santo, Brazil. We estimated population parameters and structure, measured the significance of global gametic disequilibrium and the intensity of non-random multiallelic interallelic associations and constructed a provisional synteny map using Bos taurus, the closest terrestrial mammal with a reference genome available. All microsatellite loci were polymorphic, with at least three and a maximum of ten alleles each. Allele frequencies ranged from 0.01 to 0.97. Observed heterozygosity ranged from 0.061 to 0.701. The mean inbreeding coefficient was 0.103. Three loci were in Hardy-Weinberg disequilibrium even when missing genotypes were inferred. Although 77 of the 91 possible two-locus associations were in global gametic equilibrium, we unveiled 13 statistically significant, sign-based, non-random multiallelic interallelic associations in 10 two-locus combinations with either coupling (D' values ranging from 0.782 to 0.353) or repulsion (D' values -0.517 to -1.000) forces. Most of the interallelic associations did not involve the major alleles. Thus, for either physically or non-physically linked loci, measuring the intensity of non-random interallelic associations is important for defining the evolutionary forces at equilibrium. We uncovered a small degree of genetic differentiation (FST = 0.010; P-value = 0.463) with a hierarchical clustering into one segment containing members from the southern and northern coastal regions. The data thus support the scenario of little genetic structure in the population of S. guianensis in this geographic area. [ABSTRACT FROM AUTHOR]

The mud flounder Paralichthys orbignyanus (Pleuronectiformes, Paralichthyidae) inhabits shallow waters of low salinities and mud bottoms in the temperate marine coastal regions of the Bonaerensean Ecoregion of the Argentinean Biogeographic Province in the south-western Atlantic Ocean. Specimens of P. orbignyanus were collected from Lagoa dos Patos (LDP) (southern Brazil), Mar Chiquita (MCH) and Marisol (MAR) both located in Buenos Aires (Argentina), and San Antonio Oeste (SAO) in the San Matías Gulf, Rio Negro (Argentina). A fragment of the mitochondrial DNA of the Control Region and seven microsatellite loci were characterized. In the Control Region, P. orbignyanus showed high variability, low nucleotide diversity, mild population expansion and a coalescence time of 35,000 years before the present. Flounders provided evidence of a genetic structure between the sampling sites LDP, MCH, MAR vs. SAO. On the other hand, P. orbignyanus displayed a lower to moderate contemporary genetic structure among all samples except between LDP and MCH. With no evidence of isolation by distance, this analysis supports a model of limited gene flow that is likely to be associated with a consistent larvae retention in all sampling sites. In addition, the present connectivity is ascribed to a lower migration process from SAO in the San Matías Gulf congruent with the prevailing littoral drift., (© 2022 Fisheries Society of the British Isles.)

Habitat loss and fragmentation intensify the effects of genetic drift and endogamy, reducing genetic variability of populations with serious consequences for wildlife conservation. The Harpy Eagle (Harpia harpyja) is a forest dwelling species that is considered near threatened and suffers from habitat loss in the forests of the Neotropical region. In this study, 72 historical and current samples were assessed using eight autosomal microsatellite markers to investigate the distribution of genetic diversity of the Harpy Eagle of the Amazonian and Atlantic forests in Brazil. The results showed that the genetic diversity of Harpy Eagle decreased in the regions where deforestation is intense in the southern Amazon and Atlantic Forest. [ABSTRACT FROM AUTHOR]

Aim Subterranean rodents of the genus Ctenomys are widespread in open habitats; the collared tuco-tuco, C. torquatus, has a wide range crossed by large water-courses. Based on a phylogeographical approach to investigate the riverine barrier hypothesis, we evaluated the strength of a river as a barrier and characterized the effect of large rivers in structuring distinct populations of the collared tuco-tuco. Location Grasslands of southern Brazil. Methods Sampling included 294 individuals from 33 localities throughout the geographical range of C. torquatus, especially around the main rivers. Phylogeographical patterns were estimated through two mitochondrial DNA sequences (control region and COI). Additionally, 22 microsatellite loci were surveyed to estimate the effect of rivers on population divergence through the FST index of genetic differentiation and AMOVAs. Spatial autocorrelation analyses were performed for both molecular markers. Molecular rates of change for mitochondrial DNA were estimated using fossil records and applied to Bayesian demographic analysis to test the relationship with the river geological data. Results Molecular-clock analysis estimated the time to most recent common ancestor ( TMRCA) to be c. 200 kyr and indicated a pattern of recent demographic expansion for C. torquatus. Fu's F S neutrality test was significant and negative (−13.7). High and significant FST and AMOVA among-population comparisons ( FSC) revealed highly differentiated populations, although no AMOVA groupings considering rivers as a segregating factor were significant. Spatial autocorrelation analysis revealed that isolation by distance was detected over approximately 200 km. Main conclusions The effect of the river was not proportionally larger from the headwaters to the mouth, and no population differentiation was observed after the later events of dispersal over the river or the formation of a water channel. This finding could result from the recent history of the occupation of C. torquatus in that region, combined with a dry Pleistocene climate and lower river levels. [ABSTRACT FROM AUTHOR]

This study examines the levels of gene flow, the distance and the patterns of pollen and seed dispersal, the intra-population spatial genetic structure (SGS) and the effective population size of a spatially isolated Myracrodruon urundeuva population using five microsatellite loci. The study was carried out in the Paulo de Faria Ecological Station, São Paulo State, Brazil and included the sampling and mapping of 467 adult-trees and 149 juveniles. Open-pollinated seeds (514) from 29 seed-trees were also sampled and genotyped. Significant SGS was detected in both adult ( S = 0.0269) and juveniles trees ( S = 0.0246), indicating short-distance seed dispersal. Using maternity analysis, all juveniles had the mother-tree assigned within the stand. A father-tree within the stand was also assigned for 97.3% of the juveniles and 98.4% of offspring. The average pollen dispersal distance measured in juveniles $$ \left( {\hat{\delta } = 1 3 8\pm 1 6 9 {\text{ m}},{\text{ mean}} \pm {\text{SD}}} \right) $$ and offspring $$ \left( {\hat{\delta } = 2 5 2\pm 20 4 {\text{ m}}} \right) $$ were higher than the average seed dispersal distance measured in juveniles $$ \left( {\hat{\delta } = 1 2 4\pm 1 50{\text{ m}}} \right) $$. About 70% of the pollen from juveniles and 51% from offspring traveled less than 200 m and, 72% of the seeds traveled less than 50 m. The effective population size of the studied sample indicates that the 467 adult-trees and 145 juveniles correspond respectively to 335 and 63 individuals that are neither inbred nor relatives. The results are discussed in relation to their impact on seed collection practices and genetic conservation. [ABSTRACT FROM AUTHOR]

The isolation and characterization of the first polymorphic microsatellite markers for the mangrove crab Ucides cordatus are described. The number of alleles at each locus ranged from three to 25, mean of nine alleles, in 46 crabs captured in two Brazilian mangroves. The markers averaged high levels of observed (0.709  ±  0.183) and expected (0.716  ±  0.170) heterozygosities. Departures from Hardy–Weinberg equilibrium were observed at two loci. Linkage disequilibrium tests were not significant and no evidence of null alleles was detected. All these microsatellite loci are expected to be useful in estimating fine-scale population processes of this valuable mangrove species currently subjected to excessive fishing efforts. [ABSTRACT FROM AUTHOR]

Copyright of Biotropica is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

• Adults have lower levels of inbreeding than seedlings. • Adults present intrapopulation spatial genetic structure up to 250 m. • Mating was not random due to genetic drift. • Self-fertilization results in higher ID than mating among relatives. Inbreeding in trees can result in inbreeding depression (ID), which may affect adaptation and growth of individuals that originate from self-fertilization and mating among relatives. To investigate how inbreeding can affect seed, and seedling growth, we used microsatellite loci to determine the mating system of a Hymenaea courbaril population and assess traits of seeds and seedlings for the expression of ID. Ninety-nine adult trees were mapped and genotyped and seeds collected from eight trees in a forest fragment in Sao Paulo State, Brazil. Seed length and weight were measured and germinated seedlings that had been grown under nursery conditions were genotyped and measured for height and root collar diameter (RCD) at two-month intervals (7–17 months of age). Individual fixation index was estimated for each seedling, from which they were classified as originating from mating among unrelated parents (t u), related parents (t r), or selfing (s). This classification was confirmed using paternity analysis. Phenotypic means and ID of the measured traits were calculated for each determined s , t r , and s + t r group. Mating was not random due to the occurrence of self-fertilization (1.3%), mating among relatives (5%), and correlated mating (15.6%). Biparental inbreeding was attributed to significant spatial genetic structure up to 250 m. The mean fixation index within familieswas significantly higher in seedlings (0.184) than in adults (-0.035), indicating ID from seedling to adult stages. The ID varied among seed and seedling traits throughout the study and between mating groups. Self-fertilization resulted in greater ID for seed length (8.5%) and weight (21.3%) than for t r (<7%). The ID for height and RCD of selfed individuals tended to decrease over the course of the study. The values for ID for seedling height and RCD of the s group were greater (15.8–25.6% for both traits) than for the t r group (3.1–8.2%), with a total (s + t r) similar between height (7.6–9.4%) and RCD (8.1–10.5%). We recommend that seed collection is conducted across a large number of forest fragments in the region where the restoration is to be implemented, preferably in forests that are connected or as close as possible to other remnants, to mitigate the effects of ID in future generations. Seeds must be collected from a minimum of 47 H. courbaril trees, respecting a minimum distance of 250 m between each tree to avoid collection of seeds from related individuals. [ABSTRACT FROM AUTHOR]

• Adults have lower inbreeding than juveniles. • Adults have intrapopulation spatial genetic structure. • Mean pollen dispersal distance occurs over long distances (1472 m). • Mating in the population is not random. • Logging of Swietenia macrophylla decreases the effective population size. The aims of this study were to investigate the intrapopulation spatial genetic structure (SGS) of a preserved Swietenia macrophylla population in a managed forest in Southwestern Amazon, in Acre state, Brazil, and assess the genetic parameters that underlie the conceptual framework that guides conservation and management strategies. The study was conducted in Annual Production Unit (APU) 3, where 83 adult trees (DBH ≥ 40 cm) were mapped (1650 ha). The diameter at breast height (DBH) was measured and the vascular exchange was sampled. Leaf tissues were collected from 187 juvenile individuals within a radius of 20 m of adults. The population presented high heterozygosity (H o) for adult (0.767) and juvenile (0.763) individuals, but significantly high allelic richness (R) and significantly lower fixation index (F) in adults (R = 10.3, F = 0.048) than juveniles (R = 9.3, F = 0.119). The F value significantly higher for juveniles, suggesting selection against inbred individuals between juvenile and adult life stages. SGS was detected for adults up to 300 m. Mating was mainly through outcrossing (0.97–1.0), but some crossing occurred among related trees (0.02–0.16) and were correlated (r pm = 0.06–0.22), indicating a mean effective number of pollen donors ranging from 4.5 to 18.2. Pollen dispersal distances reached 3905 m (mean of 1472 m), and mean effective pollination neighbor area of 792 ha. The effective population size (N e) within family (2.73) was lower than expected for random mating populations. The number of trees (m) required for seed collection was estimated at 55 non-inbreed and not related trees to each other. The core collection consisted of 42 (50.6%) adults across the area. These individuals should be included in seed collection as they represent 100% of the total detected genetic diversity. The inclusion of S. macrophylla on the list of species available for exploitation is not indicated, because the species requires cross breeding for its maintenance and logging reduce the N e and may negatively impact the pattern of genetic diversity. These will significantly increase the risk of genetic erosion and population extinction due to a lack of adaptive ability. Adults serve as pollen donors that ecologically and genetically contribute to the maintenance of gene flow and N e. Because it is recognized as a threatened species worldwide, and due to the fact that in areas of natural occurrence the species presents low-density and shows difficulty establishing natural regeneration, we recommend that S. macrophylla be protected from selective logging. [ABSTRACT FROM AUTHOR]

Encholirium horridum is a bromeliad that occurs exclusively on inselbergs in the Atlantic Forest biome of Brazil. These rock outcrops form natural islands that isolate populations from each other. We investigated gene flow by pollen through paternity analyses of a bromeliad population in an area of approximately 2 ha in Espírito Santo State, Brazil. To that end, seed rosettes and seedlings were genotyped using nuclear microsatellite loci. A plot was also established from the same population and specimens were genotyped to evaluate their fine-scale spatial genetic structure (SGS) through analyses of spatial autocorrelation and clonal growth. Paternity analysis indicated that 80% of the attributed progenitors of the genotyped seedlings were from inside the study area. The pollen dispersal distances within the area were restricted (mean distance of 45.5 m, varying from 3 to 156 m) and fine-scale SGS was weak (F(ij) = 0.0122, P < 0.001; Sp = 0.009). Clonal growth was found to be a rare event, supporting the monocarpy of this species., (© The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)