scholarly journals RAD-sequencing for estimating GRM-based heritability in the wild: a case study in roe deer

2018 ◽  
Author(s):  
L Gervais ◽  
C Perrier ◽  
M Bernard ◽  
J Merlet ◽  
J Pemberton ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Roe Deer ◽  
Low Frequency ◽  
Analytical Framework ◽  
Rad Sequencing ◽  
Wild Populations ◽  
Sequence Coverage ◽  
Evolutionary Potential ◽  
Heritability Estimates ◽  
The Impact

AbstractEstimating the evolutionary potential of quantitative traits and reliably predicting responses to selection in wild populations are important challenges in evolutionary biology. The genomic revolution has opened up opportunities for measuring relatedness among individuals with precision, enabling pedigree-free estimation of trait heritabilities in wild populations. However, until now, most quantitative genetic studies based on a genomic relatedness matrix (GRM) have focused on long-term monitored populations for which traditional pedigrees were also available, and have often had access to knowledge of genome sequence and variability. Here, we investigated the potential of RAD-sequencing for estimating heritability in a free-ranging roe deer population for which no prior genomic resources were available. We propose a step-by-step analytical framework to optimize the quality and quantity of the genomic data and explore the impact of the SNP calling and filtering processes on the GRM structure and GRM-based heritability estimates. As expected, our results show that sequence coverage strongly affects the number of recovered loci, the genotyping error rate and the amount of missing data. Ultimately, this had little effect on heritability estimates and their standard errors, provided that the GRM was built from a minimum number of loci (above 7000). GRM-based heritability estimates thus appear robust to a moderate level of genotyping errors in the SNP dataset. We also showed that quality filters, such as the removal of low-frequency variants, affect the relatedness structure of the GRM, generating lower h2 estimates. Our work illustrates the huge potential of RAD-sequencing for estimating GRM-based heritability in virtually any natural population.

scholarly journals Telomere heritability and parental age at conception effects in a wild avian population

2020 ◽  
Author(s):  
Alexandra Sparks ◽  
Lewis G. Spurgin ◽  
Marco van der Velde ◽  
Eleanor A. Fairfield ◽  
Jan Komdeur ◽  
...  
Keyword(s):  
Animal Models ◽  
Telomere Length ◽  
Paternal Age ◽  
Parental Age ◽  
Wild Populations ◽  
Evolutionary Potential ◽  
Confounding Variables ◽  
In The Wild ◽  
Seychelles Warbler ◽  
Heritability Estimates

Individual variation in telomere length is predictive of health and mortality risk across a range of species. However, the relative influence of environmental and genetic variation on individual telomere length in wild populations remains poorly understood. In previous studies, heritability of telomere length has primarily been calculated using parent-offspring regression, but shared environments can confound such estimates. Furthermore, associations with age and parental age at conception effects are typically not accounted for but can also bias heritability estimates. To control for these confounding variables, quantitative genetic ‘animal models’ can be used. However, the few studies on wild populations using this approach have been restricted by power. Here, we investigated the heritability of telomere length and parental age at conception effects in the Seychelles warbler using 2664 telomere length measures from 1318 birds over 20 years and a multi-generational pedigree. We found a weak negative within-paternal age at conception effect (as fathers aged, their offspring had shorter telomeres) and a weak positive between-maternal age at conception effect (females that survived to older ages had offspring with longer telomeres). While parent–offspring regressions did not detect heritability, animal models provided evidence that heritability of telomere length was low in this population. Environmental and technical variation largely influenced telomere length and would have biased heritability estimates if unaccounted for. Estimating the heritability of telomere length is complex, requiring large sample sizes and accounting for confounding effects in order to improve our understanding of the evolutionary potential of telomere length in the wild.

Long-term population dynamics of the red deer and European roe deer at the protected and not-protected areas in Mountain Crimea

2017 ◽  
Vol 7 (4) ◽  
pp. 65-72
Author(s):  
V. N. Shmagol' ◽  
V. L. Yarysh ◽  
S. P. Ivanov ◽  
V. I. Maltsev
Keyword(s):  
Population Dynamics ◽  
Protected Areas ◽  
Red Deer ◽  
Nature Reserve ◽  
Roe Deer ◽  
Precipitation Amount ◽  
Annual Precipitation ◽  
Population Number ◽  
The Impact

<p>The long-term population dynamics of the red deer (<em>Cervus elaphus</em> L.) and European roe deer (<em>Capreolus</em> <em>capreolus</em> L.) at the mountain and forest zone of Crimea during 1980-2017 is presented. Fluctuations in numbers of both species are cyclical and partly synchronous. Period of oscillations in the population of red deer is about 25 years, the average duration of the oscillation period of number of roe deer is 12.3 years. During the fluctuations in the number the increasing and fall in population number of the red deer had been as 26-47 %, and roe deer – as 22-34 %. Basing on the dada obtained we have assumed that together with large-scale cycles of fluctuations in population number of both red deer and roe deer the short cycles of fluctuations in the number of these species with period from 3.5 to 7.5 years take place. Significant differences of the parameters of cyclical fluctuations in the number of roe deer at some sites of the Mountainous Crimea: breaches of synchronicity, as well as significant differences in the duration of cycles are revealed. The greatest deviations from the average values of parameters of long-term dynamics of the number of roe deer in Crimea are noted for groups of this species at two protected areas. At the Crimean Nature Reserve the cycle time of fluctuations of the numbers of roe deer was 18 years. At the Karadag Nature Reserve since 1976 we can see an exponential growth in number of roe deer that is continued up to the present time. By 2016 the number of roe deer reached 750 individuals at a density of 437 animals per 1 thousand ha. Peculiarity of dynamics of number of roe deer at some sites proves the existence in the mountain forest of Crimea several relatively isolated groups of deer. We assumed that "island" location of the Crimean populations of red deer and European roe deer, their relatively little number and influence of permanent extreme factors of both natural and anthropogenic origination have contributed to a mechanism of survival of these populations. The elements of such a mechanism include the following features of long-term dynamics of the population: the reduction in the period of cyclic population fluctuations, while maintaining their amplitude and the appearance of additional small cycles, providing more flexible response of the population to the impact of both negative and positive environmental factors. From the totality of the weather conditions for the Crimean population of roe deer the recurring periods of increases and downs in the annual precipitation amount may have relevance. There was a trend of increase in the roe deer population during periods of increasing annual precipitation.</p>

USING FIELD DATA FOR THE EVALUATION OF THE IMPACT OF ULTRA-LOW FREQUENCY MOTIONS ON THE FATIGUE OF MOORING LINES

2019 ◽  
Author(s):  
Guilherme Borzacchiello ◽  
Carl Albrecht ◽  
Fabricio N Correa ◽  
Breno Jacob ◽  
Guilherme da Silva Leal
Keyword(s):  
Field Data ◽  
Low Frequency ◽  
Mooring Lines ◽  
The Impact

From Silent Spring to The Frog of War

2017 ◽  
Author(s):  
David K. Skelly
Keyword(s):  
Natural History ◽  
Laboratory Experiments ◽  
Wild Populations ◽  
Rachel Carson ◽  
Chemical Agents ◽  
Silent Spring ◽  
The World ◽  
History Information ◽  
Wildlife Populations ◽  
The Impact

This chapter presents two examples to demonstrate that natural history is the necessary basis of any reliable understanding of the world. More than a half century ago, Rachel Carson revolutionized the public’s view of pesticides. The foundation of her success was the careful use of natural history data, collated from across North America. The examples she assembled left little doubt that DDT and other pesticides were causing a widespread decline in birds. More recently, the case for the impact of atrazine on wildlife was based on laboratory experiments, without the advantage of natural history observations. For atrazine, natural history observations now suggest that other chemical agents are more likely to be responsible for feminization of wildlife populations. Developing expectations for scientists to collect natural history information can help to avoid over-extrapolating lab results to wild populations, a tendency often seen when those lab results conform to preconceptions about chemicals in the environment.

scholarly journals Droplet impact onto a spring-supported plate: analysis and simulations

2021 ◽  
Vol 128 (1) ◽  
Author(s):  
Michael J. Negus ◽  
Matthew R. Moore ◽  
James M. Oliver ◽  
Radu Cimpeanu
Keyword(s):  
High Speed ◽  
Flexible Substrate ◽  
Practical Importance ◽  
Hybrid Approach ◽  
Hydrodynamic Pressure ◽  
Analytical Framework ◽  
Canonical System ◽  
Linear Process ◽  
Plate Motion ◽  
The Impact

AbstractThe high-speed impact of a droplet onto a flexible substrate is a highly non-linear process of practical importance, which poses formidable modelling challenges in the context of fluid–structure interaction. We present two approaches aimed at investigating the canonical system of a droplet impacting onto a rigid plate supported by a spring and a dashpot: matched asymptotic expansions and direct numerical simulation (DNS). In the former, we derive a generalisation of inviscid Wagner theory to approximate the flow behaviour during the early stages of the impact. In the latter, we perform detailed DNS designed to validate the analytical framework, as well as provide insight into later times beyond the reach of the proposed analytical model. Drawing from both methods, we observe the strong influence that the mass of the plate, resistance of the dashpot, and stiffness of the spring have on the motion of the solid, which undergo forced damped oscillations. Furthermore, we examine how the plate motion affects the dynamics of the droplet, predominantly through altering its internal hydrodynamic pressure distribution. We build on the interplay between these techniques, demonstrating that a hybrid approach leads to improved model and computational development, as well as result interpretation, across multiple length and time scales.

scholarly journals Evaluation of P-Band SAR Tomography for Mapping Tropical Forest Vertical Backscatter and Tree Height

2021 ◽  
Vol 13 (8) ◽  
pp. 1485
Author(s):  
Naveen Ramachandran ◽  
Sassan Saatchi ◽  
Stefano Tebaldini ◽  
Mauro Mariotti d’Alessandro ◽  
Onkar Dikshit
Keyword(s):  
Tropical Forest ◽  
Vertical Profile ◽  
Mean Squared Error ◽  
Low Frequency ◽  
Tree Height ◽  
Canopy Layer ◽  
Local Maxima ◽  
Slope Correction ◽  
Compensation Approach ◽  
The Impact

Low-frequency tomographic synthetic aperture radar (TomoSAR) techniques provide an opportunity for quantifying the dynamics of dense tropical forest vertical structures. Here, we compare the performance of different TomoSAR processing, Back-projection (BP), Capon beamforming (CB), and MUltiple SIgnal Classification (MUSIC), and compensation techniques for estimating forest height (FH) and forest vertical profile from the backscattered echoes. The study also examines how polarimetric measurements in linear, compact, hybrid, and dual circular modes influence parameter estimation. The tomographic analysis was carried out using P-band data acquired over the Paracou study site in French Guiana, and the quantitative evaluation was performed using LiDAR-based canopy height measurements taken during the 2009 TropiSAR campaign. Our results show that the relative root mean squared error (RMSE) of height was less than 10%, with negligible systematic errors across the range, with Capon and MUSIC performing better for height estimates. Radiometric compensation, such as slope correction, does not improve tree height estimation. Further, we compare and analyze the impact of the compensation approach on forest vertical profiles and tomographic metrics and the integrated backscattered power. It is observed that radiometric compensation increases the backscatter values of the vertical profile with a slight shift in local maxima of the canopy layer for both the Capon and the MUSIC estimators. Our results suggest that applying the proper processing and compensation techniques on P-band TomoSAR observations from space will allow the monitoring of forest vertical structure and biomass dynamics.

scholarly journals Genetic analysis of medfly populations in an area of sterile insect technique applications

2021 ◽  
Author(s):  
Rubén Sancho ◽  
Ana Guillem-Amat ◽  
Elena López-Errasquín ◽  
Lucas Sánchez ◽  
Félix Ortego ◽  
...  
Keyword(s):  
Genetic Markers ◽  
Sterile Insect Technique ◽  
Ceratitis Capitata ◽  
Natural Populations ◽  
Low Frequency ◽  
Fruit Fly ◽  
Wild Populations ◽  
Genetic Sexing ◽  
Environmental Implications ◽  
Genetic Sexing Strains

AbstractThe sterile insect technique (SIT) is widely used in integrated pest management programs for the control of the Mediterranean fruit fly (medfly), Ceratitis capitata. The genetic interactions between the released individuals from the genetic sexing strains (GSS), used for SIT applications worldwide, and wild individuals have not been studied. Under the hypothesis that a number of Vienna GSS individuals released to the field might not be completely sterile and may produce viable offspring, we have analyzed medfly Spanish field populations to evaluate the presence of Vienna strain genetic markers. To this goal, we have used contrasted nuclear and mitochondrial genetic markers, and two novel sets of nuclear polymorphisms with the potential to be markers to discriminate between Vienna and wild individuals. Nuclear Vienna markers located on the 5th chromosome of Vienna males have been found in 2.2% (19 from 875) of the Spanish wild medfly females captured at the area where SIT is applied. In addition, a female-inherited mitochondrial Vienna marker has been found in two from the 19 females showing nuclear Vienna markers. The detection of several of these markers in single individuals represents evidence of the introgression of Vienna strain into natural populations. However, alternative explanations as their presence at low frequency in wild populations in the studied areas cannot be fully discarded. The undesired release of non-fully sterile irradiated GSS individuals into the field and their interactions with wild flies, and the potential environmental implications should be taken into account in the application of the SIT.

scholarly journals Morphological Variations of Wild Populations of Brycon dentex (Characidae, Teleostei) in the Guayas Hydrographic Basin (Ecuador). The Impact of Fishing Policies and Environmental Conditions

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1901
Author(s):  
Ana Gonzalez-Martinez ◽  
Carmen De-Pablos-Heredero ◽  
Martin González ◽  
Jorge Rodriguez ◽  
Cecilio Barba ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Environmental Conditions ◽  
Anthropogenic Activity ◽  
Freshwater Species ◽  
Fishing Pressure ◽  
Wild Populations ◽  
Morphometric Variation ◽  
Morphological Variations ◽  
Body Development ◽  
The Impact

The Guayas, located in Ecuador, is the largest basin in the Pacific Ocean and has an inventory of 123 native freshwater species. Most of these are endemic species that are threatened or at-risk due to anthropogenic activity and the modification, fragmentation, and destruction of habitats. The aim of this study was to determine the morphometric variation in three wild populations of Brycon dentex in the Guayas basin rivers and their connections to fishing management and environmental conditions. A total of 200 mature fish were captured, and 26 morphometric parameters were measured. The fishing policies (Hypothesis 1) and environmental conditions (Hypothesis 2) were considered fixed factors and were validated by t-tests. The morphological variation among the three populations (Hypothesis 3) was validated through a discriminant analysis. Fishing policies and resource management were found to generate morphological differences associated with body development. In addition, the environmental conditions were found to influence the size and structure of Brycon dentex populations. The analyzed populations were discriminated by the generated morphometric models, which differentiated Cluster 1 (Quevedo and Mocache rivers) with high fishing pressure from Cluster 2 (Pintado river) with medium–low fishing pressure. Morphometric differentiation by discriminant analysis is a direct and economic methodology that can be applied as an indicator of diversity maintenance.

scholarly journals Shift Detection in Hydrological Regimes and Pluriannual Low-Frequency Streamflow Forecasting Using the Hidden Markov Model

Water ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 2058 ◽  
Author(s):  
Larissa Rolim ◽  
Francisco de Souza Filho
Keyword(s):  
Time Series ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Extreme Events ◽  
Hidden Markov ◽  
Low Frequency ◽  
Streamflow Forecasting ◽  
Hydrologic Time Series ◽  
Low Frequency Variability ◽  
The Impact

Improved water resource management relies on accurate analyses of the past dynamics of hydrological variables. The presence of low-frequency structures in hydrologic time series is an important feature. It can modify the probability of extreme events occurring in different time scales, which makes the risk associated with extreme events dynamic, changing from one decade to another. This article proposes a methodology capable of dynamically detecting and predicting low-frequency streamflow (16–32 years), which presented significance in the wavelet power spectrum. The Standardized Runoff Index (SRI), the Pruned Exact Linear Time (PELT) algorithm, the breaks for additive seasonal and trend (BFAST) method, and the hidden Markov model (HMM) were used to identify the shifts in low frequency. The HMM was also used to forecast the low frequency. As part of the results, the regime shifts detected by the BFAST approach are not entirely consistent with results from the other methods. A common shift occurs in the mid-1980s and can be attributed to the construction of the reservoir. Climate variability modulates the streamflow low-frequency variability, and anthropogenic activities and climate change can modify this modulation. The identification of shifts reveals the impact of low frequency in the streamflow time series, showing that the low-frequency variability conditions the flows of a given year.

Sign in / Sign up

Export Citation Format

Share Document