Molecular and pedigree measures of relatedness provide similar estimates of inbreeding depression in a bottlenecked population

Individual‐based estimates of the degree of inbreeding or parental relatedness from pedigrees provide a critical starting point for studies of inbreeding depression, but in practice wild pedigrees are difficult to obtain. Because inbreeding increases the proportion of genomewide loci that are identical by descent, inbreeding variation within populations has the potential to generate observable correlations between heterozygosity measured using molecular markers and a variety of fitness related traits. Termed heterozygosity‐fitness correlations (HFCs), these correlations have been observed in a wide variety of taxa. The difficulty of obtaining wild pedigree data, however, means that empirical investigations of how pedigree inbreeding influences HFCs are rare. Here, we assess evidence for inbreeding depression in three life‐history traits (hatching and fledging success and juvenile survival) in an isolated population of Stewart Island robins using both pedigree‐ and molecular‐derived measures of relatedness. We found results from the two measures were highly correlated and supported evidence for significant but weak inbreeding depression. However, standardized effect sizes for inbreeding depression based on the pedigree‐based kin coefficients (k) were greater and had smaller standard errors than those based on molecular genetic measures of relatedness (RI), particularly for hatching and fledging success. Nevertheless, the results presented here support the use of molecular‐based measures of relatedness in bottlenecked populations when information regarding inbreeding depression is desired but pedigree data on relatedness are unavailable.     

A comparison of approaches to estimate the inbreeding coefficient and pairwise relatedness using genomic and pedigree data in a sheep population

Genome-wide SNP data provide a powerful tool to estimate pairwise relatedness among individuals and individual inbreeding coefficient. The aim of this study was to compare methods for estimating the two parameters in a Finnsheep population based on genome-wide SNPs and genealogies, separately. This study included ninety-nine Finnsheep in Finland that differed in coat colours (white, black, brown, grey, and black/white spotted) and were from a large pedigree comprising 319 119 animals. All the individuals were genotyped with the Illumina Ovine SNP50K BeadChip by the International Sheep Genomics Consortium. We identified three genetic subpopulations that corresponded approximately with the coat colours (grey, white, and black and brown) of the sheep. We detected a significant subdivision among the colour types (F _ST = 5.4%, P<0.05). We applied robust algorithms for the genomic estimation of individual inbreeding (F _SNP) and pairwise relatedness (Φ _SNP) as implemented in the programs KING and PLINK, respectively. Estimates of the two parameters from pedigrees (F _PED and Φ _PED) were computed using the RelaX2 program. Values of the two parameters estimated from genomic and genealogical data were mostly consistent, in particular for the highly inbred animals (e.g. inbreeding coefficient F>0.0625) and pairs of closely related animals (e.g. the full- or half-sibs). Nevertheless, we also detected differences in the two parameters between the approaches, particularly with respect to the grey Finnsheep. This could be due to the smaller sample size and relative incompleteness of the pedigree for them.We conclude that the genome-wide genomic data will provide useful information on a per sample or pairwise-samples basis in cases of complex genealogies or in the absence of genealogical data.     

Assessing performance of single‐sample molecular genetic methods to estimate effective population size: empirical evidence from the endangered Gochu Asturcelta pig breed

Estimating effective population size (N_e) using linkage disequilibrium (LD) information (N_e(LD)) has the operational advantage of using a single sample. However, N_e(LD) estimates assume discrete generations and its performance are constrained by demographic issues. However, such concerns have received little empirical attention so far. The pedigree of the endangered Gochu Asturcelta pig breed includes individuals classified into discrete filial generations and individuals with generations overlap. Up to 780 individuals were typed with a set of 17 microsatellites. Performance of N_e(LD) was compared with N_e estimates obtained using genealogical information, molecular coancestry (N_e(M)) and a temporal (two‐sample) method (N_e(JR)). Molecular‐based estimates of N_e exceeded those obtained using pedigree data. Estimates of N_e(LD) for filial generations F3 and F4 (17.0 and 17.3, respectively) were lower and steadier than those obtained using yearly or biannual samplings. N_e(LD) estimated for samples including generations overlap could only be compared with those obtained for the discrete filial generations when sampling span approached a generation interval and demographic correction for bias was applied. Single‐sample N_e(M) estimates were lower than their N_e(LD) counterparts. N_e(M) estimates are likely to partially reflect the number of founders rather than population size. In any case, estimates of LD and molecular coancestry tend to covary and, therefore, N_e(M) and N_e(LD) can hardly be considered independent. Demographically adjusted estimates of N_e(JR) and N_e(LD) took comparable values when: (1) the two samples used for the former were separated by one equivalent to discrete generations in the pedigree and (2) sampling span used for the latter approached a generation interval. Overall, the empirical evidence given in this study suggested that the advantage of using single‐sample methods to obtain molecular‐based estimates of N_e is not clear in operational terms. Estimates of N_e obtained using methods based in molecular information should be interpreted with caution.     

Correlated pedigree and molecular estimates of inbreeding and their ability to detect inbreeding depression in the Icelandic sheepdog, a recently bottlenecked population of domestic dogs

We examine the relationship of the inbreeding coefficient (f) and molecular estimates of inbreeding (IR, sMLH) in the Icelandic sheepdog. The breed experienced a severe genetic bottleneck and near extinction in the last century. Molecular estimates and the inbreeding coefficient are significantly correlated despite the moderate number of markers and individuals used in this study. This is most likely an effect of the extreme relatedness and relatively high variance in individual inbreeding coefficients in the population. There is a significant relationship between inbreeding (f) and the occurrence of hip dysplasia. However, the molecular measures did not detect hip dysplasia as an inbreeding effect.     

Placental alkaline phosphatase: population studies in Sardinia and data on the anthropological value of this genetic marker.

The analysis of human placental alkaline phosphatase polymorphism in Sardinia has shown a further difference in the genetic structure of this population in comparison with the populations of Continental Italy and Western Europe. Ethnic and geographic variations in world distribution of placental alkaline phosphatase gene frequencies suggest the considerable anthropological value of this genetic marker.     

Size asymmetry in intraspecific competition and the density-dependence of inbreeding depression in a natural plant population: a case study in cassava (Manihot esculenta Crantz, Euphorbiaceae)

The effects of competition on the genetic composition of natural populations are not well understood. We combined demography and molecular genetics to study how intraspecific competition affects microevolution in cohorts of volunteer plants of cassava (Manihot esculenta) originating from seeds in slash-and-burn fields of Palikur Amerindians in French Guiana. In this clonally propagated crop, genotypic diversity is enhanced by the incorporation of volunteer plants into farmers' stocks of clonal propagules. Mortality of volunteer plants was density-dependent. Furthermore, the size asymmetry of intraspecific competition increased with local clustering of plants. Size of plants was correlated with their multilocus heterozygosity, and stronger size-dependence of survival in clusters of plants, compared with solitary plants, increased the magnitude of inbreeding depression when competition was severe. The density-dependence of inbreeding depression of volunteer plants helps explain the high heterozygosity of volunteers that survive to harvest time and thus become candidates for clonal propagation. This effect could help favour the maintenance of sex in this 'vegetatively' propagated crop plant.     

On the meta-analysis of genome-wide association studies: a robust and efficient approach to combine population and family-based studies

For the meta-analysis of genome-wide association studies, we propose a new method to adjust for the population stratification and a linear mixed approach that combines family-based and unrelated samples. The proposed approach achieves similar power levels as a standard meta-analysis which combines the different test statistics or p values across studies. However, by virtue of its design, the proposed approach is robust against population admixture and stratification, and no adjustments for population admixture and stratification, even in unrelated samples, are required. Using simulation studies, we examine the power of the proposed method and compare it to standard approaches in the meta-analysis of genome-wide association studies. The practical features of the approach are illustrated with a meta-analysis of three genome-wide association studies for Alzheimer's disease. We identify three single nucleotide polymorphisms showing significant genome-wide association with affection status. Two single nucleotide polymorphisms are novel and will be verified in other populations in our follow-up study.     

The use of marker‐based relationship information to estimate the heritability of body weight in a natural population: a cautionary tale

A number of procedures have been developed that allow the genetic parameters of natural populations to be estimated using relationship information inferred from marker data rather than known pedigrees. Three published approaches are available; the regression, pair‐wise likelihood and Markov Chain Monte Carlo (MCMC) sib‐ship reconstruction methods. These were applied to body weight and molecular data collected from the Soay sheep population of St. Kilda, which has a previously determined pedigree. The regression and pair‐wise likelihood approaches do not specify an exact pedigree and yielded unreliable heritability estimates, that were sensitive to alteration of the fixed effects. The MCMC method, which specifies a pedigree prior to heritability estimation, yielded results closer to those determined using the known pedigree. In populations of low average relationship, such as the Soay sheep population, determination of a reliable pedigree is more useful than indirect approaches that do not specify a pedigree.     

Using trapped drones to assess the density of honey bee colonies: a simulation and empirical study to evaluate the accuracy of the method

1. It is often necessary to assess the density of honey bee colonies in an environment. In theory, a random sample of males obtained at a mating lek (Drone Congregation Area) can be used to infer the number of queens that contributed sons to the sample, and thereby estimate colony density based on the area from which drones are drawn to a DCA. Because of its utility and efficiency, the technique is being increasingly used. However, the accuracy of the method has never been evaluated, and there are no recommendations for sample size.
2. Here, we infer the genotypes of 322 mother queens from the genotypes of 2329 drones caught at a single DCA using the program COLONY. We then use this realistic pool of queen genotypes to generate multiple simulated data sets of drone genotypes, varying the number of queens and sons that each queen contributed to the sample.
3. We find that the technique provides an accurate estimate (<10% error) of the total number of families present in a drone sample, provided that queens contribute at least six drones to the sample on average. This threshold can be reduced when colony density is low. Non‐sampling error only becomes significant when queens contribute fewer than three sons on average across simulated samples.
4. We conclude that the technique is robust and can be used with confidence provided that the sample size is adequate.

     

Diurnal changes in the radius of a subalpine Norway spruce stem: their relation to the sap flow and their use to estimate transpiration

Diurnal changes in the stem radius of a subalpine mature Norway spruce were measured simultaneously with the flow of sap in xylem. Matric potentials in the soil were > -35 kPa. The kinetics of the flow were closely related to the changes in the radius of the stem resulting from depletion of its extensible tissues. The radius of the stem oscillated daily and, fairly independently of this, fluctuated over several days. The daily shrinkage (_d) was correlated with the daily flow through its base (Q_d). When the crown transpired little and was nearly saturated during rainy days, ASd tended to increase relative to Q_d. Using a linear relation, the estimates of flow by _d deviated less than ± 10% from the values measured by heat balance, provided that the periods of calibration in their ratio of dry to rainy days were comparable to those estimated. If the two periods differed in this respect, the estimates of flow deviated up to 42%. A quadratic relation yielded estimates that depended less on weather. It reduced maximal deviations to ±22%. Since _d additionally may represent the time pattern of the daily transpiration better than Q_d, analysing changes in the radius of stems may supplement or partly replace measurements of sap flow in stems.     

Synergistic effects of food shortage and an insecticide on a <Emphasis Type="Italic">Daphnia</Emphasis> population: rapid decline of food density at the peak of population density reduces tolerance to the chemical and induces a large population crash

Laboratory populations of cloned Daphnia magna were exposed at different population phases (growing phase, density peak, stable phase) to the insecticide carbaryl at 15 μg 1⁻¹, which was harmful to juveniles but not to adults, and their population dynamics were analyzed. The population declined most at the density peak, when not only juveniles but also many adult individuals died. To analyze the factors affecting population vulnerability to carbaryl, acute toxicity tests were conducted using Daphnia individuals of different body sizes under different food conditions. The test revealed that daphnid sensitivity to carbaryl increased greatly when food density was changed from a high food level to a low level. This food condition, of low availability, might be the condition to which the Daphnia populations were exposed at their density peak. The synergism of the negative impacts of anthropogenic and natural stresses such as insecticides and food shortage may control aquatic populations.     

Binding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: a comparative docking and MD simulation studies

Abstract

Integrin linked kinase (ILK) is a Ser/Thr kinase, which regulates various integrin mediated signaling pathways, and is involved in cell adhesion, migration and differentiation. Alteration in the ILK is responsible for abnormal functioning of the cell system, which may lead to the cancer progression and metastasis. Caffeic acid (CA) and simvastatin are used as antioxidant and possess anticancer properties. Thus, inhibiting the kinase activity of ILK by CA and simvastatin may be implicated in the cancer therapy. In this study, we have performed molecular docking followed by 100?ns MD simulations to understand the interaction mechanism of ILK protein with the CA and simvastatin. Average potential energy was found to be highest in case of ILK–CA complex (?770,949?kJ/mol). Binding free energy was found to be higher in case of simvastatin than CA. Our results indicate that simvastatin binds more effectively to the active pocket of ILK. We further performed MTT assay to understand its anticancer potential. Simvastatin shows the IC₅₀ values for HepG2 and MCF-7 as 19.18?±?0.12 and 13.84?±?0.22?µM, respectively. However, the IC₅₀ value of CA on HepG2 and MCF-7 was reported as 175.50?±?1.44 and 144.90?±?1.53?µM, respectively. Our study provides a deeper insight into the binding mechanism of simvastatin and CA to ILK, which further opens a promising channel for their implications in cancer therapy.     

Structural and dynamic differences of the estrogen receptor DNA-binding domain, binding as a dimer and as a monomer to DNA: molecular dynamics simulation studies

Molecular dynamics (MD) simulations of the estrogen receptor DNA-binding domain (ERDBD) as a dimer in complex with its DNA response element (ERE) show a significant difference in both structure and dynamics, compared to a MD simulation of monomeric ERDBD bound to its half-site response element (EREH). The C-terminal zinc binding domain (Zn_II), including a region (helix II) which is in a helical conformation in ERE-(ERDBD)₂, is considerably more flexible in EREH-ERDBD than in the dimeric complex. In EREH-ERDBD, all helical hydrogen bonds in helix II are broken and the entire Zn_II region is detached from a hydrogen bonding network that in ERE-(ERDBD)₂ connects to other parts of the protein as well as to the DNA. The regions that become flexible in EREH-ERDBD are identical to the regions where the NMR solution structure of free ERDBD is poorly ordered. This strongly suggests that dimerisation of ERDBD is required for ordering of the Zn_II region and that monomeric binding to DNA is not sufficient for the ordering. This contrasts to the glucocorticoid receptor DNA-binding domain (GRDBD) which has essentially the same mobility (uniform and limited), regardless of whether it is free as a monomer in solution, bound as a monomer to its half-site response element or in a dimeric complex with the full response element. The hydrogen bonding network that connects Zn_II with other parts of the protein and to DNA is almost identical in ERDBD and GRDBD. However, in GRDBD there is also a serine (in the N-terminal zinc coordinating region) with a central role in this network, connecting to the Zn_II region. This serine is replaced by a glycine in ERDBD and we suggest that this substitution is sufficient for destabilisation of the network, thus leading to a more flexible Zn_II region, which becomes ordered first upon forming a complex with another ERDBD and DNA. Received: 6 March 1998 / Revised version: 22 June 1998 / Accepted: 2 September 1998     

Quantitative studies of the non-productive binding of lysozyme to partially N-acetylated chitosans: Binding of large ligands to a one-dimensional binary lattice studied by a modified McGhee and von Hippel model

This paper considers the non-productive (inhibitory) binding of chitosans to lysozyme from chicken egg white. Chitosans are linear, binary heteropolysaccharides consisting of 2-acetamido-2-deoxy-β-d-glucose (GlcNAc; A-unit) and 2-amino-2-deoxy-β-d-glucose (GlcN, D-unit). The active site cleft of lysozyme can bind six consecutive sugar residues in subsites named A–F, and specific binding of chitosan sequences to lysozyme occurs with A-units in subsite C. Chitosans with different fractions of A-units (F_A) induced nearly identical changes in the ¹H NMR spectrum of lysozyme upon binding, and the concentration of bound lysozyme could be determined. The data were analysed using a modified version of the McGhee and von Hippel model for binding of large ligands to one-dimensional homogeneous lattices. The average value of the dissociation constant for different sequences that may bind to lysozyme (K^ave_D) was estimated, as well as the number of chitosan units covered by lysozyme upon binding. K^ave_D decreased with increasing F_A-values at pH* 3 and 4.5, while the opposite was true at pH* 5.5. Contributions from different hexamer sequences to K^ave_D of the chitosans were considered, and the data revealed interesting features with respect to binding of lysozyme to partially N-acetylated chitosans. The relevance of the present data with respect to understanding lysozyme degradation kinetics of chitosans is discussed.     

Genetic variation and population structure in a threatened species,the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions

The Utah prairie dog (Cynomys parvidens), listed as threatened under the United States Endangered Species Act, was the subject of an extensive eradication program throughout its range during the 20th century. Eradication campaigns, habitat destruction/fragmentation/conversion, and epizootic outbreaks (e.g., sylvatic plague) have reduced prairie dog numbers from an estimated 95,000 individuals in the 1920s to approximately 14,000 (estimated adult spring count) today. As a result of these anthropogenic actions, the species is now found in small isolated sets of subpopulations. We characterized the levels of genetic diversity and population genetic structure using 10 neutral nuclear microsatellite loci for twelve populations (native and transplanted) representative of the three management designated “recovery units,” found in three distinct biogeographic regions, sampled across the species' range. The results indicate (1) low levels of genetic diversity within colonies (H_e = 0.109–0.357; H_o = 0.106‐ 0.313), (2) high levels of genetic differentiation among colonies (global F_ST = 0.296), (3) very small genetic effective population sizes, and (4) evidence of genetic bottlenecks. The genetic data reveal additional subdivision such that colonies within recovery units do not form single genotype clusters consistent with recovery unit boundaries. Genotype cluster membership support historical gene flow among colonies in the easternmost West Desert Recovery Unit with the westernmost Pausaugunt colonies and among the eastern Pausaugunt colonies and the Awapa Recovery unit to the north. In order to maintain the long‐term viability of the species, there needs to be an increased focus on maintaining suitable habitat between groups of existing populations that can act as connective corridors. The location of future translocation sites should be located in areas that will maximize connectivity, leading to maintenance of genetic variation and evolutionary potential.     

Bigheaded carps (<Emphasis Type="Italic">Hypophthalmichthys</Emphasis> spp.) at the edge of their invaded range: using hydroacoustics to assess population parameters and the efficacy of harvest as a control strategy in a large North American river

The threat posed by bigheaded carps (Hypophthalmichthys spp.) to novel ecosystems has focused efforts on preventing further range expansion; upstream progression in the Illinois River is a major concern due to its connection with the uninvaded Great Lakes. In addition to an electric barrier system, commercial harvest of silver carp (H. molitrix) and bighead carp (H. nobilis) in the upper river is intended to reduce propagule pressure and prevent range expansion. To quantify demographics and evaluate harvest efficacy, the upper river was sampled between 2012 and 2015 using mobile hydroacoustic methods. Reach-specific densities, size structures and species compositions varied interannually but the advancing population was characterized longitudinally as small-bodied, silver carp-dominated at the highest densities downstream, shifting to large-bodied, bighead carp-dominated at the low-density population front. The use of hydroacoustic sampling for harvest evaluation was validated in backwater lakes; there was a significant positive correlation between density estimates and the corresponding harvest catch-per-unit-effort of bigheaded carps. Localized densities of bigheaded carps were reduced by up to 64.4 % immediately post-harvest but generally rebounded within weeks. However, annual sampling of the entire upper river indicated that density of bigheaded carps decreased by over 40 % (between 2012 and 2013) and subsequently remained stable (between 2013 and 2014). The annual harvest of bigheaded carps increased during this period (from 45,192 to 102,453 individuals), in years of contrasting discharge conditions. At this spatiotemporal scale, harvest appears to have contributed to initial reduction, and subsequent maintenance of, bigheaded carps density levels, but discharge likely plays an important role (e.g., through immigration) in determining the extent of its impact. Mobile hydroacoustic sampling enabled robust quantification of the population over varying spatial scales and density gradients, highlighting the potential of this approach as an assessment tool for invasive fishes in riverine environments.     

A mutation at the Ala122 position of acetohydroxyacid synthase (AHAS) located on chromosome 6D of wheat: improved resistance to imidazolinone and a faster assay for marker assisted selection

A new mutation at the acetohydroxyacid synthase (AHAS) locus on chromosome 6D of wheat was analyzed in detail because it conferred an improved resistance to the imidazolinone group of herbicides. Sequence analysis showed that the mutation was at the Ala122 position (A122T), a position in AHAS which has not to date been identified in imidazolinone resistant wheat lines even though the position has been identified in other plants and is associated with resistance. An allele-specific assay for the mutation (in the wheat line Brookton-8) was developed and used in a genetic analysis. Two mapping populations were analysed and the doubled haploid progeny from the cross Brookton-8 × Clearfield STL proved to be most informative. The AHAS^Ala122 mutation (A122T) was allelic to the AHAS^Ser653 mutation (S653N) in Clearfield STL (Imi1, on chromosome 6D) and hence was assigned to the chromosome 6D locus. The analysis of the doubled haploid lines in the mapping population demonstrated the greater resistance conferred by the A122T mutation because lines from the same cross and carrying either the A122T or S653N mutations could be directly compared. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.