Average Ho Research Articles

Genic simple sequence repeat markers for measuring genetic diversity in a native food crop: a case study of Australian Kunzea pomifera F.Muell. (muntries)

Kunzea pomifera F.Muell. (muntries) is a native food crop in Australia that produces spicy apple-flavoured berries. Orchards were established in the 1990s using a variety of wild-collected selections. No published records are currently available of formal plant breeding although the Rivoli Bay selection is the most widely planted. DNA markers are needed to reliably assess genetic diversity and validate plant selections, however genomic resources of K. pomifera are not available. Initially, based on the large MYB gene family, eight MYB gene fragments were amplified and cloned using a degenerate PCR primer strategy. Targeted amplicon sequencing was subsequently used to evaluate diversity of 19 K. pomifera plants and this revealed the presence of single nucleotide polymorphisms and simple sequence repeats (SSRs). Three genic SSR markers were developed from K. pomifera MYB gene fragments and another three genic SSRs were successfully transferred from K. pulchella (Lindl.) A. S. George. A high transfer rate (75%) was obtained due to selecting SSRs in genic regions (introns or intergenic regions) and using Eucalyptus grandis W.Hill sequences to identify conserved regions. The six SSRs were highly polymorphic with observed heterozygosity (Ho) (average Ho = 0.63) and polymorphic information content (PIC) (average PIC = 0.54). Using the six genic SSRs, 15 unique genotypes were identified from the K. pomifera collections in two orchards. Importantly, plants in a new diversity panel were genotyped and suspected mis-labeling events confirmed. The genic SSRs and approach developed will benefit marker assisted selection programs by increasing the proportion of genic markers that could be linked to important horticultural traits.

Evolution of nickel hyperaccumulation and serpentine adaptation in the Alyssum serpyllifolium species complex.

Metal hyperaccumulation is an uncommon but highly distinctive adaptation found in certain plants that can grow on metalliferous soils. Here we review what is known about evolution of metal hyperaccumulation in plants and describe a population-genetic analysis of the Alyssum serpyllifolium (Brassicaceae) species complex that includes populations of nickel-hyperaccumulating as well as non-accumulating plants growing on serpentine (S) and non-serpentine (NS) soils, respectively. To test whether the S and NS populations belong to the same or separate closely related species, we analysed genetic variation within and between four S and four NS populations from across the Iberian peninsula. Based on microsatellites, genetic variation was similar in S and NS populations (average Ho=0.48). The populations were significantly differentiated from each other (overall FST=0.23), and the degree of differentiation between S and NS populations was similar to that within these two groups. However, high S versus NS differentiation was observed in DNA polymorphism of two genes putatively involved in adaptation to serpentine environments, IREG1 and NRAMP4, whereas no such differentiation was found in a gene (ASIL1) not expected to play a specific role in ecological adaptation in A. serpyllifolium. These results indicate that S and NS populations belong to the same species and that nickel hyperaccumulation in A. serpyllifolium appears to represent a case of adaptation to growth on serpentine soils. Further functional and evolutionary genetic work in this system has the potential to significantly advance our understanding of the evolution of metal hyperaccumulation in plants.

Microsatellite primers for two threatened orchids in Florida: Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae)

Premise of the study:The Million Orchid Project at Fairchild Tropical Botanic Garden is an initiative to propagate native orchids for reintroduction into Miami’s urban landscapes. The aim of this study was to develop microsatellites for Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae).Methods and Results:Ten microsatellites were developed for each species. For E. tampensis sampled from the natural population, allele numbers ranged from one to four, with an average observed heterozygosity (Ho) of 0.314 and average expected heterozygosity (He) of 0.281. For the individuals from cultivation, allele numbers ranged from one to six, with an average Ho of 0.35 and an average He of 0.224. For C. punctatum, allele numbers ranged from one to three, with an average Ho of 0.257 and an average He of 0.272.Conclusions:These microsatellites will be used to assess the genetic diversity of natural and cultivated populations with the intention of guiding genetic breeding under the Million Orchid Project.

Genetic structure and diversity of the black-throated finch (Poephila cincta) across its current range

Understanding the patterns of population connectivity and level of genetic diversity can facilitate the identification of both ecologically relevant populations and the spatial scales at which conservation management may need to focus. We quantified genetic variation within and among populations of black-throated finches across their current distribution. To quantify genetic structure and diversity, we genotyped 242 individuals from four populations using 14 polymorphic microsatellite markers and sequenced 25 individuals based on a 302-base-pair segment of mitochondrial control region. We found modest levels of genetic diversity (average allelic richness r = 4.37 ± 0.41 (standard error) and average heterozygosity HO = 0.42 ± 0.040 (standard error)) with no bottleneck signature among sampled populations. We identified two genetic groups that represent populations of two subspecies based on Bayesian clustering analysis and low levels of genetic differentiation based on pairwise genetic differentiation statistics (all FST, RST and Nei’s unbiased D values <0.1). Our data suggest that genetic exchange occurs among sampled populations despite recent population declines. Conservation efforts that focus on maintaining habitat connectivity and increasing habitat quality to ensure a high level of gene flow on a larger scale will improve the species’ ability to persist in changing landscapes. Conservation management should also support continuous monitoring of the bird to identify any rapid population declines as land-use intensification occurs throughout the species’ range.

SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces

We report here the development of 75 SSR markers for Bambara groundnut through various sequencing approaches and the subsequent utilization of these SSR markers and other marker types (DArT Arrays) for the analysis of genetic diversity, population structure and the selection of pure lines from landraces. To assess the level of genetic diversity in Bambara groundnut landrace collections, 68 and 201 polymorphic SSR and DArT markers, respectively, were assayed against 24 single individual seed from a core collection of landraces. Polymorphic information content (PIC) ranged from 0.08 to 0.89 with an average of 0.42 across all SSR polymorphic markers, with observed (Ho) and expected (He) heterozygosity of 0.01 and 0.5 respectively. For the population structure analysis, 12 SSR markers selected as highly polymorphic from the initial screen were assayed against 123 landrace accessions. The average PIC across the 12 SSR was 0.66 with an average Ho of 0.02 and an inbreeding coefficient (f) of 0.98, suggesting that seed derived from a single plant essentially represents an unselected variety. Based on the low level of Ho and high f observed in the landrace samples, a subset of 35 genotypes derived from the landraces were advanced for field trials in Botswana and scored for 37 phenotypic traits. These 35 individual genotypes were ranked for agronomic performance based on yield component factors and other qualitative traits after field evaluation. Five genotypes with good yield potential and adaptability were recommended as potential varieties for Botswanan agro-ecology.

Population Genetic Analysis of the Rice Stem Borer, Chilo suppressalis, in the South China

Genetic variation and patterns of genetic differentiation of the rice stem borer, Chilo suppressalis (Lepidoptera: Pyralidae), from the South China were analyzed using 6 microsatellite markers and two partial mtDNA (cox1 and cox2) regions. All of the 6 microsatellite loci were polymorphic in the studied seven populations. The allelic richness per population ranged between 5.67 and 14.00, and average HE and HO values were 0.6246-0.8329 and 0.2634-0.6061, respectively. As the mitochondrial genome is a single genetic locus, we only present results for the concatenated data set (cox1 plus cox2 gene sequences, 513 bp). The concatenated data showed high level of genetic diversity and there are 23 variable polymorphic sites among the 513 sites in concatenated data. Nearly all of (20 of 21) pairwise FST comparisons among populations showed genetic differentiation with moderate to high pairwise FST values based on microsatellite markers. However, for the mtDNA data, most of the seven populations did not show significant differentiation with other populations. The differences of population differentiation obtained with the two different genetic markers could be mainly attributed to the different mutation rates of microsatellite and mtDNA. There was not genetic structure existed in these studied populations based on microsatellite loci and mtDNA data. The analysis based on network, mismatch distribution, Tajima's D and FS indicated that the studied populations were from the recent same ancestor or the same refuge and followed by a sudden demographic expansion condition.

Development of 24 new microsatellite markers in the Crested Serpent Eagle (Spilornis cheela hoya)

Twenty-four microsatellite markers were developed for the Crested Serpent Eagle (Spilornis cheela hoya) composing a new marker set. The markers were tested on 61 Crested Serpent Eagle individuals. The number alleles ranged from 2 to 8 per locus (average = 3.8), and the effective number of alleles ranged from 1.13 to 6.07 (average = 2.34). In the new marker set, there were 11 markers with high polymorphism (PIC > 0.5), and the average HE and HO over all loci was 0.50 and 0.49, respectively. The results showed that the new marker set was highly polymorphic as an individual genetic marker compared to the existing cross-species markers previously used for population genetic structure monitoring of the Taiwan Crested Serpent Eagle. In conclusion, the microsatellite marker set developed can be applied as a molecular tool to investigate the genetic structure or phylogeny of the Crested Serpent Eagle.

Variabilidad genética de poblaciones en cautiverio de <i>Crocodylus moreletii</i> (Crocodylia: Crocodylidae) mediante el uso de marcadores microsatelitales.

Crocodylus moreletii, an extinction threatened species, represents an emblem for tropical ecosystems in Mexico. Surprisingly, there is a lack of information about their genetic constitution, which should be evaluated for a proper management ex situ and for making decisions on the release of crocodiles into natural habitats. The aim of this study was to characterize and compare the genetic variability of four populations of C. moreletii (two wild versus two born ex situ). Through PCR were amplified seven microsatellite polymorphic loci, however a heterozygote deficit, diminished by the presence of null alleles, was found in the populations (average Ho=0.02). The AMOVA indicated that the highest proportion of genetic variability is within populations, and a limited genetic differentiation among populations (average F(ST)=0.03), probably due to high inbreeding index (average F(IS)=0.97). When comparing the genetic variability between and within other crocodilian species, we found that in C. moreletii is well below those reported. We concluded that the limited genetic variability in ex situ born populations is probably due to a founder effect derived from the social structure of their progenitors, and by the bottleneck effect, inferred by the limited effective population size, that historically characterizes their natural distribution in wild populations.

Development of microsatellite markers in an ungulate mammal, the Formosan serow (Capricornis swinhoei)

Sixteen microsatellite markers were isolated from Formosan serow (Capricornis swinhoei) to compose a new marker set. Analysis of the Formosan serow population in the Taipei zoo yielded a mean number alleles = 6.4 with a range from 3 to 11, and the mean of the effective number of alleles = 3.6 with a range from 2.0 to 6.1. In the marker set, there were 14 markers with high polymorphism (PIC > 0.5), and the average HE and HO over all loci was 0.642 and 0.701, respectively. The results showed that the new marker set was not only highly polymorphic but also powerful in the individual and parentage identification compared to the existing cross-species markers. In conclusion, the markers developed in this study could be applied as molecular tools to investigate the genetic structure or phylogeny of the Formosan serow in the future.

Measurements and ab initio molecular dynamics simulations of the high temperature ferroelectric transition in hexagonal RMnO3

Measurements of the structure of hexagonal RMnO3 [R = rare earths (Ho) and Y] for temperatures significantly above the ferroelectric transition temperature (TFE) were conducted to determine the nature of the transition. The local and long range structural measurements were complemented by ab initio molecular dynamics simulations. With respect to the Mn sites in YMnO3 and HoMnO3, we find no large atomic (bond distances or thermal factors), electronic structure changes, or rehybridization on crossing TFE from local structural methods. The local symmetry about the Mn sites is preserved. With respect to the local structure about the Ho sites, a reduction of the average Ho–O bond with increased temperature is found. Ab initio molecular dynamics calculations on HoMnO3 reveal the detailed motions of all ions. Above ∼900 K there are large displacements of the Ho, O3, and O4 ions along the z axis which reduce the buckling of the MnO3/O4 planes. The changes result in O3/O4 ions moving to toward central points between pairs of Ho ions on the z axis. These structural changes make the coordination of Ho sites more symmetric thus extinguishing the electric polarization. At significantly higher temperatures, rotation of the MnO5 polyhedra occurs without a significant change in electric polarization. The Born effective charge tensor is found to be highly anisotropic at the O sites but does not change appreciably at high temperatures.

Genetic diversity of Oreopanax xalapensis (Araliaceae) in the Highlands of Chiapas

The genetic diversity of a species determines its ability to respond to environmental changes, thus their knowledge can be important for designing strategies for forest restoration. This study analyzes the diversity and genetic structure of five populations of Oreopanax xalapensis in the Highlands of Chiapas. This species is being used for restoration of the montane cloud forests into the region, but unknown levels of genetic variation in natural populations where seeds are obtained. We used 18 enzymatic loci screened by electrophoresis in cellulose acetate. Genotype frequencies were used to calculate the allelic frequency and obtained the following estimates of genetic diversity: proportion of polymorphism, observed (HO) and expected heterocigosity (HE); and average number of alleles. The FST statistic was used to estimate the level of genetic differentiation among subpopulations. The average number of alleles per locus was between 1.8 and 2.0; the proportion of loci polymorphic ranged from 66 to 100%. Average HO was 0.362, and HE = 0.379. The degree of structure was significantly high (FST = 0.214), the indirect estimate of gene flow among subpopulations was Nm = 5.0 individuals per generation. Subpopulations of O. xalapensis are genetically diverse and are structured; this implies that for an effective restoration practice should be considered the collection of seeds of all populations for a better representation of genetic diversity.

Lake Michigan air quality: The 1994–2003 LADCO Aircraft Project (LAP)

The goal of the 1994 to 2003 LADCO Airplane Project (LAP) was to study ozone formation over Lake Michigan so that equitable regional control strategies could be devised. This paper for the first time documents LAP in the peer-reviewed literature. Dye et al. (1995) found that the atmosphere over Lake Michigan is stable in the summer due to the airwater temperature difference, which creates an efficient reaction chamber for ozone formation. They also hypothesize that the southwest winds characteristic of ozone-conducive conditions transport ozone further north over the lake before it crosses the shoreline onto land. This statistical analysis of LAP data support the hypothesis of Dye et al. Below 200 m above the lake, ozone formation is VOC-limited in the morning and becomes NO x limited in the afternoon. Above 200 m, ozone formation is NO x -limited throughout the day. The onshore NO x and VOC diurnal cycles peak during the early morning rush hour and are clearly linked to traffic patterns. Over the lake, VOC and NO y concentrations peak during the mid-morning rather than the early morning, supporting the hypothesis that the land breeze transports VOC and NO y over the lake. The diurnal NO x pattern over Lake Michigan is less clearly defined than the VOC pattern possibly as a result of emissions from five coal-burning power plants located on the Lake Michigan shoreline. Using a “photochemical clock” model, we estimate the climatological average hydroxyl radical concentration over the lake to be (9.43 ± 5.88) × 106 molecule cm −3 near Chicago and (8.43 ± 3.68) × 106 molecule cm −3 near Milwaukee. ► First report of a decade-long airplane study of ozone episodes over Lake Michigan. ► O 3 formation is first VOC-limited then NO x -limited at low altitudes over the lake. ► Average HO • concentration was estimated using a “photochemical clock”.

SSR-based molecular analysis of economically important Turkish apricot cultivars

Turkey is not only the main apricot (Prunus armeniaca) producer and exporter in the world, but it also has a wide variety of apricot germplasms, owing to its close proximity to the centers of apricot origin. However, there is little or no genetic information on many apricot cultivars that are extensively cultivated in Turkey. We examined the genetic relatedness of 25 Turkish and four exotic apricot cultivars using SSR (simple sequence repeat) markers that were either previously developed for apricot, or for peach (P. persica), a close relative of apricot. Allele diversity (with an average allele number of 6.37) at the SSR loci and the heterozygosity rates (with an average Ho value of 0.648) of these cultivars were found to be higher than in previous studies that used the same loci for apricot. This fact might be attributed to the analysis of different numbers of accessions in the different studies. No correlations were found between the genetic relatedness and the geographical distributions of these cultivars. The data reported here will assist in the prevention of confusions in the apricot propagation and breeding in Turkey. The findings can also be directly compared with other studies that used the same SSR markers on apricot.

Genetic variability analysis in five populations of the sea cucumber Stichopus (Apostichopus) japonicus from China, Russia, South Korea and Japan as revealed by microsatellite markers

AbstractThe genetic structure of populations of the sea cucumber Stichopus (Apostichopus) japonicus was investigated using 10 microsatellite markers. In all, 152 individuals from five natural populations were collected from Aomori, Japan (JA and JR), Yosu, South Korea (KY), Dalian, China (CD) and Vladivostock, Russia (RV). A total of 145 alleles were found at 10 loci. The number of alleles per locus ranged from 9 at PSC03 to 20 at SCZ06, with an average of 14.5. Average Ho and He ranged from 0.260 (JR) to 0.434 (JA) and from 0.654 (RV) to 0.778 (KY), respectively. No significant differences at A, Ho and He were found, indicating similar genetic diversity in the five populations. A single allele was found at the PSC05 locus in the RV population. Of the 50 loci, 42 significantly deviated from Hardy–Weinberg equilibrium, all showing heterozygote deficiency. The genetic distances were all relatively great, ranging from 0.497 (between JA and KY) to 1.029 (between KY and JR). This suggests the five populations are genetically distinct. Cluster analysis indicated that JA, KY and CD form one branch and RV and JR another in the UPGMA tree. A hypothesis is proposed for the evolution of the Japanese red sea cucumbers and the genetic relationship among the populations.

A panel of polymorphic EST-derived microsatellite loci for the bay scallop (Argopecten irradians)

A panel of polymorphic EST-derived microsatellite loci for the bay scallop (Argopecten irradians)

High genetic diversity and no inbreeding in the endangered copper redhorse,Moxostoma hubbsi(Catostomidae, Pisces): the positive sides of a long generation time

The evolutionary potential of a species is determined by its genetic diversity. Thus, management plans should integrate genetic concerns into active conservation efforts. The copper redhorse (Moxostoma hubbsi) is an endangered species, with an endemic distribution limited to the Richelieu River and a short section of the St Lawrence River in Quebec, Canada. The population, gradually fragmented since 1849, is characterized by a decline in population size and a lack of recruitment. A total of 269 samples were collected between 1984 and 2004 and genotyped using 22 microsatellite loci, which indicated that these fish comprise a single population, with a global F(ST) value of only 0.0038. Despite a small census size ( approximately 500), a high degree of genetic diversity was observed compared to common values for freshwater fishes (average number of 12.5 alleles/locus and average HO of 0.77 +/- 0.08). No difference was observed between expected and observed pairwise values of relatedness (r(xy): -0.00013 +/- 0.11737), suggesting an outbred population. Long-term Ne was estimated at 4476 whereas contemporary Ne values ranged from 107 to 568, suggesting a pronounced yet gradual demographic decline of the population, as no bottleneck could be detected for the recent past. By means of simulations, we estimated Ne would need to remain at more than approximately 400 to retain 90% of the genetic diversity over 100 years. Overall, these observations corroborate other recent empirical studies confirming that long generation times may act as a buffering effect contributing to a reduction in the pace of genetic diversity erosion in threatened species.

A Model for Trivalent Actinides in Media Containing High Carbonate Concentrations − Structural Characterization of the Lanthanide Tetracarbonate [Co(NH3)6][Na(μ-H2O)(H2O)4]2[Ho(CO3)4]·4H2O

The identity of the limiting HoIII species in aqueous solutions with high carbonate concentrations has been determined to be Ho(CO3)45−. Single crystals of [Co(NH3)6][Na(μ−H2O)(H2O)4]2[Ho(CO3)4]·4H2O were obtained by the addition of [Co(NH3)6]3+ to an aqueous 0.04 M solution of HoIII in 2.1 M Na2CO3. The asymmetric unit contains the anion, [Ho(CO3)4]5−, a [Co(NH3)6]3+ cation and two Na+ cations, which are bound to H2O molecules in an edge-sharing bioctahedral geometry. The [Ho(CO3)4]5− anion is eight coordinate with four bidentate carbonate ligands bound to the Ho atom. The molecule has essentially C2v symmetry with two coplanar carbonates making a vane, which is perpendicular to a similar vane produced by the other two carbonate ligands. An alternative way to this view molecule is through the geometry of the C atoms, which are found in a distorted tetrahedron. The average Ho−O distance was determined to be 2.361(5) Å, while the average Ho−C distance was 2.784(6) Å. The IR and Raman spectra were determined in both the solid state and solution in order to confirm the solution speciation. The Raman data show a single CO32− stretch for the solid at 1062 cm−1. The solution data show multiple peaks with the most prominent being at 1048 cm−1, which is consistent with the literature reports of an equilibrium mixture. The IR data for the solids confirm the X-ray results showing bidentate carbonate ligands by the splitting of the ν3 band of the CO32−. The crystal data for [Co(NH3)6][Na(μ-H2O)(H2O)4]2[Ho(CO3)4]·4H2O are as follows: monoclinic space group P2/n, a = 8.7091(5) Å, b = 10.8744(6) Å, c = 15.7971(9) Å, β = 93.117(1)°, Z = 2, R1 = 0.0307, wR2 = 0.0756.

HO cycle in 1997 and 1998 over the southern Indian Ocean derived from CO, radon, and hydrocarbon measurements made at Amsterdam Island

A new empirical method for the derivation of average HO radical concentrations is presented. The method is based on estimation of CO lifetime through the relative variability of CO and Rn measurements, and hydrocarbon measurements are used to independently determine the relative effects of chemistry and dynamics. Data from Amsterdam Island (37°S, 77°E), a remote site in the southern Indian Ocean, are used to calculate annual and daily HO levels for 1997 and 1998. A seasonal variation in calculated daily HO, consistent with seasonally changing photolysis rates, with maxima in summer and minima in winter is also derived which is comparable but slightly lower than the most recent zonal mean HO estimates of Spivakovsky et al. [2000]. The calculated annual HO shows a decrease from 2.7×105 molecule cm−3 in 1997 to 0.8×105 molecule cm−3 in 1998, possibly as a result of El Niño related meteorological changes. The empirically calculated HO correlates with temperature and relative humidity measured at the island but anticorrelates strongly with CO and to a lesser extent with O3. The limitations and improvements to this method are discussed. The method has potential for long‐term monitoring of HO changes over areas upwind from remote sites.

Variability‐lifetime relationship for organic trace gases: A novel aid to compound identification and estimation of HO concentrations

In this study we report aircraft‐borne measurements of organic species made during March 1998 in Surinam, an unpolluted region on the northeast coast of South America Measurements included the following: CO by tunable diode laser; a wide variety of organics including acetone, acetonitrile, and isoprene by proton transfer mass spectrometry (PTR‐MS); and nonmethane hydrocarbon measurements by gas chromatography‐flame ionization detection. Here we compare the standard deviation of the natural logarithm of the mixing ratio (Sigma_lnX) to the estimated lifetime of these species. This relationship has been used to support identification of masses measured by the PTR‐MS; ascertain the consistency and quality of hydrocarbon measurement data; and to provide information concerning sinks of important trace species. A selection of the data is used to indirectly determine an average HO concentration of 2.0×105 molecules cm−3 along the back trajectory for air encountered during the Large‐Scale Biosphere‐Atmosphere Experiment in Amazonia‐Cooperative LBA Airborne Regional Experiment (LBA‐CLAIRE) measurement campaign between 0–1 km over the tropical rain forest. The lower than expected HO concentration derived could have been caused by significant atmospheric or oceanic photochemical production of acetone and MEK along the back trajectory.

Synthesis and crystal structure of [Y(NO3)3(OH2)3].(Me2-16-crown-5).H2O

The complex [Y(NO3)3(OH2)3]·(Me2-16-crown-5)·H2O has been prepared and its crystal and molecular structure determined using single crystal X-ray diffraction. The colorless crystals belong to the monoclinic space group P21/n with Z = 4. Lattice parameters are a = 10.420(1), b = 17.257(3), c = 14.646(2) A, β = 96.79(1)°, V = 2615.1(6) A3. The yttrium(III) ion is nine-coordinate, bonded to three bidentate nitrate groups and three water molecules. The average Y–O(nitrate) and Y–O(water) distances are 2.42(3) and 2.33(1) A, respectively. The average HO–H···O hydrogen bonded separation is 2.767A.