Low genetic diversity and potential inbreeding in an isolated population of alder buckthorn (Frangula alnus) following a founder effect.
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ABSTRACT:
SUBMITTER: Finlay CMV
PROVIDER: S-EPMC5462792 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients (F) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate.When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.
| S-EPMC5145906 | biostudies-other
Project description:After its recent rediscovery, the Hula painted frog (Latonia nigriventer) has remained one of the world's rarest and least understood amphibian species. Together with its apparently low dispersal capability and highly disturbed niche, the low abundance of this living fossil calls for urgent conservation measures. We used 18 newly developed microsatellite loci and four different models to calculate the effective population size (Ne) of a total of 125 Hula painted frog individuals sampled at a single location. We compare the Ne estimates to the estimates of potentially reproducing adults in this population (Nad) determined through a capture-recapture study on 118 adult Hula painted frogs captured at the same site. Surprisingly, our data suggests that, despite Nad estimates of only ~234-244 and Ne estimates of ~16.6-35.8, the species appears to maintain a very high genetic diversity (HO?=?0.771) and low inbreeding coefficient (FIS?=?-0.018). This puzzling outcome could perhaps be explained by the hypotheses of either genetic rescue from one or more unknown Hula painted frog populations nearby or by recent admixture of genetically divergent subpopulations. Independent of which scenario is correct, the original locations of these populations still remain to be determined.
| S-EPMC5882862 | biostudies-other
Project description:Background and aimsMany invasive species severely threaten native biodiversity and ecosystem functioning. One of the most prominent questions in invasion genetics is how invasive populations can overcome genetic founder effects to establish stable populations after colonization of new habitats. High native genetic diversity and multiple introductions are expected to increase genetic diversity and adaptive potential in the invasive range. Our aim was to identify the European source populations of Frangula alnus (glossy buckthorn), an ornamental and highly invasive woody species that was deliberately introduced into North America at the end of the 18th century. A second aim of this study was to assess the adaptive potential as an explanation for the invasion success of this species.MethodsUsing a set of annotated single-nucleotide polymorphisms (SNPs) that were assigned a putative function based on sequence comparison with model species, a total of 38 native European and 21 invasive North American populations were subjected to distance-based structure and assignment analyses combined with population genomic tools. Genetic diversity at SNPs with ecologically relevant functions was considered as a proxy for adaptive potential.Key resultsPatterns of invasion coincided with early modern transatlantic trading routes. Multiple introductions through transatlantic trade from a limited number of European port regions to American urban areas led to the establishment of bridgehead populations with high allelic richness and expected heterozygosity, allowing continuous secondary migration to natural areas.ConclusionsTargeted eradication of the urban populations, where the highest genetic diversity and adaptive potential were observed, offers a promising strategy to arrest further invasion of native American prairies and forests.
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Project description:Alnus glutinosa is an actinorhizal plant that fixes N via actinomycetes. Compared to other trees, A. glutinosa is more resistant to environmental stress and able to uptake soil nutrients more easily. Alnus glutinosa grows well not only in natural stands but also in degraded environment or soil in need of restoration. Changes in the contents of selected macro-, micro-, and non-nutrient elements in the leaves of A. glutinosa during the vegetation season were monitored in the Ore Mountains (Czech Republic), an area affected by extreme air pollution in the past. Decreased foliar content of N, P, K, and Cu, and increased content of Ca, Mn, Zn, and Al were observed; the content of other elements (S, Mg, Pb, and Cd) varied during the growing season or remained constant. From the viewpoint of nutrition, the content of N, S, Ca, and Mg macroelements was adequate; concentrations of P and K were low. Excessive amounts of Mn and Zn were measured, and the level of Cu was good. Non-nutrient elements Pb and Cd were present at the background level, and the level of Al was high. N/P, N/Ca, N/Mg, and Ca/Mg ratios were balanced, S/N value showed the lack of S, and N/K ratio indicated low content of K, which caused also suboptimal K/Ca and K/Mg values. The P/Al ratio varied from balanced to lower values. The content of individual elements and monitored changes were influenced by the amount of elements in the soil, moisture conditions, foliage phenology, and altitude.
| S-EPMC10834585 | biostudies-literature
Project description:The Thoroughbred horse has played an important role in both sporting and economic aspects of society since the establishment of the breed in the 1700s. The extensive pedigree and phenotypic information available for the Thoroughbred horse population provides a unique opportunity to examine the effects of 300 years of selective breeding on genetic load. By analysing the relationship between inbreeding and racing performance of 135,572 individuals, we found that selective breeding has not efficiently alleviated the Australian Thoroughbred population of its genetic load. However, we found evidence for purging in the population that might have improved racing performance over time. Over 80% of inbreeding in the contemporary population is accounted for by a small number of ancestors from the foundation of the breed. Inbreeding to these ancestors has variable effects on fitness, demonstrating that an understanding of the distribution of genetic load is important in improving the phenotypic value of a population in the future. Our findings hold value not only for Thoroughbred and other domestic breeds, but also for small and endangered populations where such comprehensive information is not available.
| S-EPMC5906619 | biostudies-literature
Project description:Alnus viridis (Chaix) DC., green alder, is a fast-growing shrub that grows expansively in the European mountainside. In Poland, A. viridis naturally occurs only in the Bieszczady Mountains (south-eastern part of the country), above the upper forest border. In this study, we assessed the potential of green alder to expand in post-farming areas in the Bieszczady Mountains. We investigated the effects of topographical, climatic, and edaphic characteristics of four various study sites on the physiological and morphological properties of A. viridis leaves in order to answer the question whether the growth of plants in lower positions improves their physiological condition to such an extent that it increases the species invasiveness. This is the first comprehensive ecophysiological study of this species to be carried out in this part of Europe. The photochemical efficiency of PSII, the chlorophyll content, and leaf 13C and 15N discrimination were analyzed. On the basis of leaf radiation reflection, coefficients such as reflectance indices of anthocyanins, carotenoids, flavonoids (ARI2, CRI1, FRI), photochemical index of reflection (PRI), and the water band index (WBI) were calculated. We observed favorable physiological effects in A. viridis plants growing in locations below the upper forest border compared to plants growing in higher locations. As a result, A. viridis may become an invasive species and disturb the phytocoenotic balance of plant communities of the altitudinal zones in the Polish Western Carpathians.
| S-EPMC7825132 | biostudies-literature
Project description:Phenolic compounds isolated from plant biomass consist of bioactive components showing a wide range of benefits for humans, including antioxidant, antimicrobial or anti-inflammatory effects. This paper presents the potential value of black alder (Alnus glutinosa (L.) Gaertn. (Betulaceae)) bark for the production of biologically active substances, despite its current use as a low value fuel source. Most of the extraction methods employ neat organic solvents to obtain extracts with a high antioxidant potential from biomass. The aim of this work is to show the advantages and disadvantages of the extraction process by taking into account the principles of 'green chemistry' and replacing the organic solvents with 'green' solvent water. Using the advantages of accelerated solvent extraction (ASE), it has been shown that the use of deionized water has the prospect of replacing organic solvents. In the case of the one-step water extraction, the total polyphenol content (TPC) varies from 0.55 to 0.62 Gallic acid equivalent (GAE) g/g in the extracts, depending on the temperature, whereas with the result of the sequential extraction with the organic solvents, the TPC content of the 40% (v:v) ethanol extracts ranges from 0.39 to 0.61 GAE g/g, depending on the temperature. The influence of the total polyphenol content and the total proanthocyanidin content on the antioxidant activity is shown. The antioxidant activity (IC50, mg/L) of the extracts obtained with the organic solvents in the (2,2-diphenyl-1-picrylhydrazyl) DPPH• test varies from 4.05 to 9.58, depending on the temperature in the range of 70-150 °C, respectively, while the results obtained with the deionized water showed promising results in the range of 6.33-7.36 in the temperature range of 70-150 °C, respectively. The extraction with the deionized water showed that approximately 90% of the substances in the extracts obtained with the organic solvents by sequential extraction are possible to obtain as deionized water extracts.
| S-EPMC8621986 | biostudies-literature
Project description:Although asexual reproduction via clonal propagation has been proposed as the principal reproductive mechanism across parasitic protozoa of the Leishmania genus, sexual recombination has long been suspected, based on hybrid marker profiles detected in field isolates from different geographical locations. The recent experimental demonstration of a sexual cycle in Leishmania within sand flies has confirmed the occurrence of hybridisation, but knowledge of the parasite life cycle in the wild still remains limited. Here, we use whole genome sequencing to investigate the frequency of sexual reproduction in Leishmania, by sequencing the genomes of 11 Leishmania infantum isolates from sand flies and 1 patient isolate in a focus of cutaneous leishmaniasis in the Çukurova province of southeast Turkey. This is the first genome-wide examination of a vector-isolated population of Leishmania parasites. A genome-wide pattern of patchy heterozygosity and SNP density was observed both within individual strains and across the whole group. Comparisons with other Leishmania donovani complex genome sequences suggest that these isolates are derived from a single cross of two diverse strains with subsequent recombination within the population. This interpretation is supported by a statistical model of the genomic variability for each strain compared to the L. infantum reference genome strain as well as genome-wide scans for recombination within the population. Further analysis of these heterozygous blocks indicates that the two parents were phylogenetically distinct. Patterns of linkage disequilibrium indicate that this population reproduced primarily clonally following the original hybridisation event, but that some recombination also occurred. This observation allowed us to estimate the relative rates of sexual and asexual reproduction within this population, to our knowledge the first quantitative estimate of these events during the Leishmania life cycle.
| S-EPMC3894156 | biostudies-literature
Project description:Inbreeding can affect fitness-related traits at different life history stages and may interact with environmental variation to induce even larger effects. We used genetic parentage assignment based on 22 microsatellite loci to determine a 25 year long pedigree for a newly established island population of moose with 20-40 reproducing individuals annually. We used the pedigree to calculate individual inbreeding coefficients and examined for effects of individual inbreeding (f) and heterozygosity on fitness-related traits. We found negative effects of f on birth date, calf body mass and twinning rate. The relationship between f and calf body mass and twinning rate were found to be separate but weaker after accounting for birth date. We found no support for an inbreeding effect on the age-specific lifetime reproductive success of females. The influence of f on birth date was related to climatic conditions during the spring prior to birth, indicating that calves with a low f were born earlier after a cold spring than calves with high f. In years with a warm spring, calf f did not affect birth date. The results suggest that severe inbreeding in moose has both indirect effects on fitness through delayed birth and lower juvenile body mass, as well as separate direct effects, as there still was a significant relationship between f and twinning rate after accounting for birth date and body mass as calf. Consequently, severe inbreeding as found in the study population may have consequences for population growth and extinction risk.
| S-EPMC3853567 | biostudies-literature
Project description:Background:Experiencing an adequate amount of cold temperatures over winter is necessary for many temperate tree species to break dormancy and flower in spring. Thus, changes in winter and spring temperatures associated with climate change may influence when trees break dormancy and flower in the future. There have been several experimental studies that have quantified the effectiveness of cold temperatures for chilling requirements for vegetative budburst of temperate trees; however, there are few experimental studies addressing the chilling requirements for reproductive budburst of trees, as it is difficult to place reproductively mature trees in temperature-controlled environments. Methods:To identify how changing temperatures associated with climate change may impact reproductive phenology, we completed a temperature-controlled growth chamber experiment using cuttings of reproductive branches of red alder (Alnus rubra), one of the most widespread hardwood tree species of the Pacific Northwest, USA. The purpose of this study was to examine how colder (4 °C) and warmer (9 °C) winter temperature regimes influenced the timing of reproductive budburst of red alder cuttings in spring. We also compared the date of budburst of cuttings to that of branches from intact trees. Results:We found that cuttings flowered earlier after pretreatment with a 4 °C winter temperature regime than after a 9 °C winter temperature regime. We found no significant differences between the timing of male budburst of cuttings exposed to ambient conditions compared to male budburst of branches from intact trees. We used our experimental data to estimate a "possibility-line" that shows the accumulated chilling and forcing temperatures necessary prior to reproductive budburst of red alder. Discussion:This study provides a preliminary indication that warmer winters with climate change may not be as effective as colder winters for satisfying chilling temperature requirements of a Northwest hardwood tree species.
| S-EPMC6161696 | biostudies-literature