Distribution of protein variation in skipjack tuna (Katsumonus pelamis) from the central and south-west Pacific

1983 ◽  
Vol 34 (2) ◽  
pp. 231 ◽  
Author(s):  
BJ Richardson
Keyword(s):  
Isolation By Distance ◽  
Low Frequency ◽  
Frequency Variation ◽  
Skipjack Tuna ◽  
Average Heterozygosity ◽  
Gene Frequencies ◽  
Protein Variation ◽  
Guanine Deaminase ◽  
Distance Model ◽  
East West

Forty-two loci were electrophoretically surveyed for protein variation in the skipjack tuna. A new polymorphism in guanine deaminase was found as well as low-frequency variation in glucosephosphate isomerase and adenosine deaminase. Average heterozygosity for the species was 0 032. The gene frequencies at four variable loci for 70 sample sets, each of approximately 100 animals, collected at locations throughout the South Pacific Commission region, are given. East-west clines in allele frequencies for carboxylesterase and guanine deaminase occur across the study area. There is also within-area heterogeneity in allele frequency at these loci. Previously proposed discrete-stock models and a new isolation-by-distance model for the population structure of skipjack tuna are examined in the light of the genetic data.

scholarly journals Spatial autocorrelation analysis of migration and selection.

Genetics ◽  
1989 ◽  
Vol 121 (4) ◽  
pp. 845-855
Author(s):  
R R Sokal ◽  
G M Jacquez ◽  
M C Wooten
Keyword(s):  
Spatial Autocorrelation ◽  
Gene Frequency ◽  
Isolation By Distance ◽  
Spatial Autocorrelation Analysis ◽  
Autocorrelation Analysis ◽  
Gene Frequencies ◽  
Selection Gradients ◽  
Surface Migration ◽  
Distance Model ◽  
Components Analysis

Abstract We test various assumptions necessary for the interpretation of spatial autocorrelation analysis of gene frequency surfaces, using simulations of Wright's isolation-by-distance model with migration or selection superimposed. Increasing neighborhood size enhances spatial autocorrelation, which is reduced again for the largest neighborhood sizes. Spatial correlograms are independent of the mean gene frequency of the surface. Migration affects surfaces and correlograms when immigrant gene frequency differentials are substantial. Multiple directions of migration are reflected in the correlograms. Selection gradients yield clinal correlograms; other selection patterns are less clearly reflected in their correlograms. Sequential migration from different directions and at different gene frequencies can be disaggregated into component migration vectors by means of principal components analysis. This encourages analysis by such methods of gene frequency surfaces in nature. The empirical results of these findings lend support to the inference structure developed earlier for spatial autocorrelation analysis.

scholarly journals A Low frequency Southern Sky Survey Using the Mauritius Radio Telescope

2002 ◽  
Vol 199 ◽  
pp. 25-31
Author(s):  
N. Udaya Shankar
Keyword(s):  
Radio Telescope ◽  
Low Frequency ◽  
Fourier Synthesis ◽  
North East ◽  
The North ◽  
Sky Survey ◽  
Correlation Receiver ◽  
Complex Correlation ◽  
Right Ascension ◽  
East West

The Mauritius Radio Telescope (MRT) is a Fourier synthesis instrument which has been built to fill the gap in the availability of deep sky surveys at low radio frequencies in the southern hemisphere. It is situated in the north-east of Mauritius at a southern latitude of 20°.14 and an eastern longitude of 57°.73. The aim of the survey with the MRT is to contribute to the database of southern sky sources in the declination range −70° ≤ δ ≤ −10°, covering the entire 24 hours of right ascension, with a resolution of 4' × 4'.6sec(δ + 20.14°) and a point source sensitivity of 200 mJy (3σ level) at 151.5 MHz.MRT is a T-shaped non-coplanar array consisting of a 2048 m long East-West arm and a 880 m long South arm. In the East-West arm 1024 fixed helices are arranged in 32 groups and in the South arm 16 trolleys, with four helices on each, which move on a rail are used. A 512 channel, 2-bit 3-level complex correlation receiver is used to measure the visibility function. At least 60 days of observing are required for obtaining the visibilities up to the 880 m spacing. The calibrated visibilities are transformed taking care of the non-coplanarity of the array to produce an image of the area of the sky under observation.This paper will describe the telescope, the observations carried out so far, a few interesting aspects of imaging with this non-coplanar array and present results of a low resolution survey (13' × 18') covering roughly 12 hours of right ascension, and also present an image with a resolution of 4' × 4'.6sec(δ + 20.14°) made using the telescope.

scholarly journals Complex Principal Component Analysis of Antarctic Ice Sheet Mass Balance

2021 ◽  
Vol 13 (3) ◽  
pp. 480
Author(s):  
Jingang Zhan ◽  
Hongling Shi ◽  
Yong Wang ◽  
Yixin Yao
Keyword(s):  
Principal Component Analysis ◽  
Ice Sheet ◽  
Low Frequency ◽  
Principal Component ◽  
Equatorial Pacific ◽  
Mass Change ◽  
Frequency Variation ◽  
Periodic Signal ◽  
Time Frequency ◽  
The Antarctic

Ice sheet changes of the Antarctic are the result of interactions among the ocean, atmosphere, and ice sheet. Studying the ice sheet mass variations helps us to understand the possible reasons for these changes. We used 164 months of Gravity Recovery and Climate Experiment (GRACE) satellite time-varying solutions to study the principal components (PCs) of the Antarctic ice sheet mass change and their time-frequency variation. This assessment was based on complex principal component analysis (CPCA) and the wavelet amplitude-period spectrum (WAPS) method to study the PCs and their time-frequency information. The CPCA results revealed the PCs that affect the ice sheet balance, and the wavelet analysis exposed the time-frequency variation of the quasi-periodic signal in each component. The results show that the first PC, which has a linear term and low-frequency signals with periods greater than five years, dominates the variation trend of ice sheet in the Antarctic. The ratio of its variance to the total variance shows that the first PC explains 83.73% of the mass change in the ice sheet. Similar low-frequency signals are also found in the meridional wind at 700 hPa in the South Pacific and the sea surface temperature anomaly (SSTA) in the equatorial Pacific, with the correlation between the low-frequency periodic signal of SSTA in the equatorial Pacific and the first PC of the ice sheet mass change in Antarctica found to be 0.73. The phase signals in the mass change of West Antarctica indicate the upstream propagation of mass loss information over time from the ocean–ice interface to the southward upslope, which mainly reflects ocean-driven factors such as enhanced ice–ocean interaction and the intrusion of warm saline water into the cavities under ice shelves associated with ice sheets which sit on retrograde slopes. Meanwhile, the phase signals in the mass change of East Antarctica indicate the downstream propagation of mass increase information from the South Pole toward Dronning Maud Land, which mainly reflects atmospheric factors such as precipitation accumulation.

scholarly journals Null expectation of spatial correlograms under a stochastic process of genetic divergence with small sample sizes

2000 ◽  
Vol 23 (4) ◽  
pp. 739-743 ◽  
Author(s):  
Mariana Pires de Campos Telles ◽  
José Alexandre Felizola Diniz-Filho
Keyword(s):  
Stochastic Process ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Small Sample ◽  
Group Method ◽  
Gene Frequencies ◽  
Exponential Relationship ◽  
Local Populations ◽  
Pair Group

An Ornstein-Uhlenbeck process was used to simulate the exponential relationship between genetic divergence and geographic distances, as predicted by stochastic processes of population differentiation, such as isolation-by-distance, stepping-stone or coalescence models. These simulations were based only on the spatial coordinates of the local populations that defined a spatial unweighted pair-group method using arithmetic averages (UPGMA) link among them. The simulated gene frequency surfaces were then analyzed using spatial autocorrelation procedures and Nei's genetic distances, constructed with different numbers of variables (gene frequencies). Stochastic divergence in space produced strong spatial patterns at univariate and mutivariate levels. Using a relatively small number of local populations, the correlogram profiles varied considerably, with Manhattan distances greater than those defined by other simulation studies. This method allows one to establish a range of correlogram profiles under the same stochastic process of spatial divergence, thereby avoiding the use of unnecessary explanations of genetic divergence based on other microevolutionary processes.

scholarly journals The Genome Segments of Bluetongue Virus Differ in Copy Number in a Host-Specific Manner

2020 ◽  
Vol 95 (1) ◽  
Author(s):  
Yannis Moreau ◽  
Patricia Gil ◽  
Antoni Exbrayat ◽  
Ignace Rakotoarivony ◽  
Emmanuel Bréard ◽  
...  
Keyword(s):  
Bluetongue Virus ◽  
Expression Regulation ◽  
Viral Gene ◽  
Frequency Variation ◽  
Gene Frequencies ◽  
Biting Midges ◽  
Main Hypothesis ◽  
A Genome ◽  
Reverse Transcription Quantitative Pcr ◽  
Virus Expression

ABSTRACT Genome segmentation is mainly thought to facilitate reassortment. Here, we show that segmentation can also allow differences in segment abundance in populations of bluetongue virus (BTV). BTV has a genome consisting in 10 segments, and its cycle primarily involves periodic alternation between ruminants and Culicoides biting midges. We have developed a reverse transcription-quantitative PCR (RT-qPCR) approach to quantify each segment in wild BTV populations sampled in both ruminants and midges during an epizootic. Segment frequencies deviated from equimolarity in all hosts. Interestingly, segment frequencies were reproducible and distinct between ruminants and biting midges. Beyond a putative regulatory role in virus expression, this phenomenon could lead to different evolution rates between segments. IMPORTANCE The variation in viral gene frequencies remains a largely unexplored aspect of within-host genetics. This phenomenon is often considered to be specific to multipartite viruses. Multipartite viruses have segmented genomes, but in contrast to segmented viruses, their segments are each encapsidated alone in a virion. A main hypothesis explaining the evolution of multipartism is that, compared to segmented viruses, it facilitates the regulation of segment abundancy, and the genes the segments carry, within a host. These differences in gene frequencies could allow for expression regulation. Here, we show that wild populations of a segmented virus, bluetongue virus (BTV), also present unequal segment frequencies. BTV cycles between ruminants and Culicoides biting midges. As expected from a role in expression regulation, segment frequencies tended to show specific values that differed between ruminants and midges. Our results expand previous knowledge on gene frequency variation and call for studies on its role and conservation beyond multipartite viruses.

Chloroplast DNA phylogeography in long-lived Huon pine, a Tasmanian rain forest conifer

2008 ◽  
Vol 38 (6) ◽  
pp. 1576-1589 ◽  
Author(s):  
Catherine M. Clark ◽  
Ignazio Carbone
Keyword(s):  
Nucleotide Diversity ◽  
Isolation By Distance ◽  
Population Bottlenecks ◽  
Base Pairs ◽  
Distance Model ◽  
History Of ◽  
Lagarostrobos Franklinii ◽  
Tasmanian Endemic ◽  
Western Portion

Genealogy based methods were used to estimate phylogeographic history for a Tasmanian endemic conifer, Huon pine ( Lagarostrobos franklinii (Hook. f.) Quinn). DNA from trees in eight populations was sequenced using three chloroplast primers (trnS–trnT, trnD–trnT, and psbC–trnS). Mean nucleotide diversity was low (π = 0.000 93 ± 0.000 06) from 892 base pairs of sequence, but varied in stands from 0.0 to 0.001 15. Two of the five haplotypes were widely distributed, but the most frequently occurring haplotype was found only in the western portion of the range. Population structure was highly significant among populations overall (GST = 0.261, where GST is the coefficient of gene differentiation, and p ≤ 0.0001), and there were indications of significant isolation by distance (p ≤ 0.022). Populations exhibited the highest levels of differentiation between the southeastern and northwestern watersheds. Estimates of migration between populations obtained using both parametric and nonparametric methods indicated levels of gene flow consistent with an isolation by distance model. Nested clade analysis demonstrated a pattern of genetic diversity in Huon pine that is consistent with a history of range expansion. The exceptionally low level of nucleotide diversity, haplotype distribution, and paleoecological data are congruent with a history of long-term range reduction, population bottlenecks, and subsequent colonization events from refugial areas.

Allozyme Evidence of Genetic Differentiation Between Populations of Hediste Diversicolor (Polychaeta: Nereididae) from the Western Mediterranean

1996 ◽  
Vol 76 (3) ◽  
pp. 637-647 ◽  
Author(s):  
M. Abbiati ◽  
F. Maltagliati
Keyword(s):  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Western Mediterranean ◽  
Allozyme Electrophoresis ◽  
Isolated Populations ◽  
Hediste Diversicolor ◽  
Dispersal Capacity ◽  
Two Samples ◽  
Distance Model ◽  
Limited Dispersal

The occurrence of genetic differentiation among western Mediterranean Hediste diversicolor (Polychaeta: Nereididae) populations was assessed by allozyme electrophoresis on cellulose acetate. Seventeen loci were analysed in four populations. The level of the genetic variability was markedly low (mean HL range: 0.014–0.034), but comparable to that of other brackish water nereidids. The values of Nei genetic distance index (D) confirm the existence of genetic differentiation between the geographically isolated populations at Venice, Elba, Navicelli and Serchio D range: 0.128–0.356). However, the two samples from Serchio and Navicelli, ~15 km apart, were not genetically different (D=0·00005). The level of genetic differentiation in H. diversicolor populations followed the isolation-by-distance model. Reduced gene flow among H. diversicolor populations may be explained by its limited dispersal capacity and the eco-physiological barriers that occur between different brackish habitats.

scholarly journals Limited evidence for sardine and anchovy asynchrony: re-examining an old story

2020 ◽  
Vol 287 (1922) ◽  
pp. 20192781
Author(s):  
Margaret C. Siple ◽  
Timothy E. Essington ◽  
Lewis A. K. Barnett ◽  
Mark D. Scheuerell
Keyword(s):  
Time Series ◽  
Food Webs ◽  
Low Frequency ◽  
Single Species ◽  
The Other ◽  
Generalist Predators ◽  
Frequency Variation ◽  
Limited Evidence ◽  
Short Time Series ◽  
Short Time

Asynchronous fluctuations in abundance between species with similar ecological roles can stabilize food webs and support coexistence. Sardine ( Sardinops spp.) and anchovy ( Engraulis spp.) have long been used as an example of this pattern because low-frequency variation in catches of these species appears to occur out of phase, suggesting that fisheries and generalist predators could be buffered against shifts in productivity of a single species. Using landings data and biomass and recruitment estimates from five regions, we find that species do not have equivalent peak abundances, suggesting that high abundance in one species does not compensate for low abundance in the other. We find that globally there is a stronger pattern of asynchrony in landings compared to biomass, such that landings data have exaggerated the patterns of asynchrony. Finally, we show that power to detect decadal asynchrony is poor, requiring a time series more than twice the length of the period of fluctuation. These results indicate that it is unlikely that the dynamics of these two species are compensatory enough to buffer fisheries and predators from changes in abundance, and that the measurements of asynchrony have largely been a statistical artefact of using short time series and landings data to infer ecology.

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