Ecological correlates of population genetic structure: a comparative approach using a vertebrate metacommunity

Identifying ecological factors associated with population genetic differentiation is important for understanding microevolutionary processes and guiding the management of threatened populations. We identified ecological correlates of several population genetic parameters for three interacting species (two garter snakes and an anuran) that occupy a common landscape. Using multiple regression analysis, we found that species interactions were more important in explaining variation in population genetic parameters than habitat and nearest-neighbour characteristics. Effective population size was best explained by census size, while migration was associated with differences in species abundance. In contrast, genetic distance was poorly explained by the ecological correlates that we tested, but geographical distance was prominent in models for all species. We found substantially different population dynamics for the prey species relative to the two predators, characterized by larger effective sizes, lower gene flow and a state of migration-drift equilibrium. We also identified an escarpment formed by a series of block faults that serves as a barrier to dispersal for the predators. Our results suggest that successful landscape-level management should incorporate genetic and ecological data for all relevant species, because even closely associated species can exhibit very different population genetic dynamics on the same landscape.

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The broad-snouted caiman population recovery in Argentina. A case of genetics conservation

Amphibia-Reptilia ◽

10.1163/15685381-00003123 ◽

2017 ◽

Vol 38 (4) ◽

pp. 411-424 ◽

Cited By ~ 2

Author(s):

Patricia Susana Amavet ◽

Eva Carolina Rueda ◽

Juan César Vilardi ◽

Pablo Siroski ◽

Alejandro Larriera ◽

...

Keyword(s):

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Population Genetic ◽

Genetic Parameters ◽

Population Recovery ◽

Santa Fe ◽

Effective Population ◽

Population Genetic Parameters ◽

The Impact

Caiman latirostriswild populations have suffered a drastic reduction in the past, and for that reason, a management and monitoring plan was applied since 1990 in Santa Fe, Argentina in order to achieve population recovery. Although ranching system has a noteworthy success in terms of population size recovering, there is no information about the estimation of population genetic parameters. In particular, the consequence of the bottleneck underwent by these populations has not been assessed. We evaluated variability and genetic structure ofC. latirostrispopulations from Santa Fe through time, using microsatellites and mitochondrial DNA. Population genetic parameters were compared among four sites and three different periods to assess the impact of management activities, and effective population size was estimated in order to detect bottleneck events. We observed an increase in microsatellite variability and low genetic variability in mitochondrial lineages through time. Variability estimates are similar among sites in each sampling period; and there is scarce differentiation among them. The genetic background of each sampling site has changed through time; we assume this fact may be due to entry of individuals of different origin, through management and repopulation activities. Moreover, taking into account the expected heterozygosity and effective population size values, it can be assumed that bottleneck events indeed have occurred in the recent past. Our results suggest that, in addition to increasing population size, genetic variability of the species has been maintained. However, the information is still incomplete, and regular monitoring should continue in order to arrive to solid conclusions.

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The Limits to Estimating Population-Genetic Parameters with Temporal Data

Genome Biology and Evolution ◽

10.1093/gbe/evaa056 ◽

2020 ◽

Vol 12 (4) ◽

pp. 443-455

Author(s):

Michael Lynch ◽

Wei-Chin Ho

Keyword(s):

Population Genetic ◽

Genetic Parameters ◽

Natural Populations ◽

Estimation Methods ◽

Frequency Change ◽

Sampling Variance ◽

Effective Population ◽

Closed Population ◽

Temporal Variance ◽

Population Genetic Parameters

Abstract The ability to obtain genome-wide sequences of very large numbers of individuals from natural populations raises questions about optimal sampling designs and the limits to extracting information on key population-genetic parameters from temporal-survey data. Methods are introduced for evaluating whether observed temporal fluctuations in allele frequencies are consistent with the hypothesis of random genetic drift, and expressions for the expected sampling variances for the relevant statistics are given in terms of sample sizes and numbers. Estimation methods and aspects of statistical reliability are also presented for the mean and temporal variance of selection coefficients. For nucleotide sites that pass the test of neutrality, the current effective population size can be estimated by a method of moments, and expressions for its sampling variance provide insight into the degree to which such methodology can yield meaningful results under alternative sampling schemes. Finally, some caveats are raised regarding the use of the temporal covariance of allele-frequency change to infer selection. Taken together, these results provide a statistical view of the limits to population-genetic inference in even the simplest case of a closed population.

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Structure and genetic variability of the Mexican Sardo Negro breed

Ciência Rural ◽

10.1590/0103-8478cr20210116 ◽

2022 ◽

Vol 52 (5) ◽

Author(s):

Joel Domínguez-Viveros ◽

Antonio Reyes-Cerón ◽

Juan Fernando Saiz-Pineda ◽

Cesar Villegas-Gutiérrez ◽

Guadalupe Nelson Aguilar-Palma ◽

...

Keyword(s):

Genetic Variability ◽

Population Genetic ◽

Genetic Parameters ◽

Inbreeding Coefficient ◽

Structure Evolution ◽

Effective Number ◽

Effective Population ◽

Population Genetic Parameters ◽

Additive Genetic Relationship ◽

Over Time

ABSTRACT: This study analyzed the Sardo Negro breed pedigree (41,521 animals registered from 1958 to 2019) to determine its structure, evolution, and genetic variability (GV). The population genetic parameters evaluated were effective number of founders (fe) and ancestors (fa), pedigree integrity, additive genetic relationship (AGR); number of complete generations (NCG), maximum generations traced (NMGT), and equivalent complete generations (NECG); effective population size (Ne), inbreeding coefficient (F), and generation interval (GI). The average GI was 7.45 years. A total of 7,804 founders and 4,856 ancestors were identified for a fe of 185 and a fa of 97. The average and maximum values of NCG, NECG, and NMGT were 1.6 and 5.0, 2.5 and 6.5, 4.3 and 12, with Ne estimates of 15.9, 25.9, and 69.0, respectively. The increase in F, linked to Ne, ranged from 0.72% to 3.1% per generation. The average values for F and AGR were 3.6% and 1.0%, respectively. The proportion of inbred individuals was 32.0%, with F values ranging from 0.01 to 62.2% and an average of 11.3%. The rate of inbred population was 1.3% per year. The annual rate of AGR was 0.04%. For the continuity and projection of the breed, the evolution of F as a function of Ne and the possible implications of the selection schemes must be considered. The genetic variability sustained over time results from the Ne.

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Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations

Bioinformatics ◽

10.1093/bioinformatics/btz498 ◽

2019 ◽

Vol 36 (1) ◽

pp. 221-231 ◽

Cited By ~ 1

Author(s):

Yasuhiro Kojima ◽

Hirotaka Matsumoto ◽

Hisanori Kiryu

Keyword(s):

Allele Frequency ◽

Population Genetic ◽

Genetic Parameters ◽

Sequence Data ◽

Expectation Maximization Algorithm ◽

Supplementary Information ◽

Effective Population ◽

Forward Equation ◽

Population Genetic Parameters ◽

Frequency Changes

Abstract Motivation Evolve and resequence (E&R) experiments show promise in capturing real-time evolution at genome-wide scales, enabling the assessment of allele frequency changes SNPs in evolving populations and thus the estimation of population genetic parameters in the Wright–Fisher model (WF) that quantify the selection on SNPs. Currently, these analyses face two key difficulties: the numerous SNPs in E&R data and the frequent unreliability of estimates. Hence, a methodology for efficiently estimating WF parameters is needed to understand the evolutionary processes that shape genomes. Results We developed a novel method for estimating WF parameters (EMWER), by applying an expectation maximization algorithm to the Kolmogorov forward equation associated with the WF model diffusion approximation. EMWER was used to infer the effective population size, selection coefficients and dominance parameters from E&R data. Of the methods examined, EMWER was the most efficient method for selection strength estimation in multi-core computing environments, estimating both selection and dominance with accurate confidence intervals. We applied EMWER to E&R data from experimental Drosophila populations adapting to thermally fluctuating environments and found a common selection affecting allele frequency of many SNPs within the cosmopolitan In(3R)P inversion. Furthermore, this application indicated that many of beneficial alleles in this experiment are dominant. Availability and implementation Our C++ implementation of ‘EMWER’ is available at https://github.com/kojikoji/EMWER. Supplementary information Supplementary data are available at Bioinformatics online.

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Population genetic characteristics of horse chestnut in Serbia

Archives of Biological Sciences ◽

10.2298/abs1301001o ◽

2013 ◽

Vol 65 (1) ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Mirjana Ocokoljic ◽

Dragica Vilotic ◽

Mirjana Sijacic-Nikolic

Keyword(s):

Population Genetic ◽

Genetic Parameters ◽

Individual Variability ◽

Horse Chestnut ◽

Statistical Parameters ◽

Genetic Characteristics ◽

Different Populations ◽

Growth Phenotype ◽

Population Genetic Parameters ◽

Cultivated Populations

The general population genetic characteristics of cultivated horse chestnut trees excelling in growth, phenotype characteristics, type of inflorescence, productivity and resistance to the leafminer Cameraria ohridella Deschka and Dimic were analyzed in Serbia. The analyzed population genetic parameters point to fundamental differences in the genetic structure among the cultivated populations in Serbia. The study shows the variability in all properties among the populations and inter-individual variability within the populations. The variability and differential characteristics were assessed using statistical parameters, taking into account the satisfactory reflection of the hereditary potential. The assessed differences in the vitality and evolution potential of different populations can determine the methods of horse chestnut gene pool collection, reconstruction and improvement.

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Inferring Population Genetic Parameters: Particle Filtering, HMM, Ripley’s K-Function or Runs of Homozygosity?

Lecture Notes in Computer Science - Algorithms in Bioinformatics ◽

10.1007/978-3-319-43681-4_19 ◽

2016 ◽

pp. 234-245

Author(s):

Svend V. Nielsen ◽

Simon Simonsen ◽

Asger Hobolth

Keyword(s):

Particle Filtering ◽

Population Genetic ◽

Genetic Parameters ◽

Runs Of Homozygosity ◽

Ripley’S K Function ◽

Ripley’S K ◽

Ripley's K ◽

Population Genetic Parameters ◽

K Function

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Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates

Genome ◽

10.1139/g10-006 ◽

2010 ◽

Vol 53 (4) ◽

pp. 302-310 ◽

Cited By ~ 32

Author(s):

Doris Herrmann ◽

Bénédicte N. Poncet ◽

Stéphanie Manel ◽

Delphine Rioux ◽

Ludovic Gielly ◽

...

Keyword(s):

Genetic Diversity ◽

Fragment Length ◽

Population Genetic ◽

Selection Criteria ◽

Genetic Parameters ◽

Data Set ◽

Marker Selection ◽

Length Polymorphisms ◽

Amplified Fragment Length Polymorphisms ◽

Population Genetic Parameters

A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.

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Use of RAPD analyses to estimate population genetic parameters in the alfalfa leaf-cutting bee, Megachile rotundata

Genome ◽

10.1139/g96-083 ◽

1996 ◽

Vol 39 (4) ◽

pp. 655-663 ◽

Cited By ~ 13

Author(s):

Rui Lu ◽

Gerald H. Rank

Keyword(s):

Genetic Distance ◽

Population Genetic ◽

Rapd Markers ◽

Genetic Parameters ◽

Megachile Rotundata ◽

Isolated Populations ◽

Leaf Cutting ◽

Nucleotide Divergence ◽

Alfalfa Leaf ◽

Population Genetic Parameters

RAPD analyses were performed on five geographically isolated populations of Megachile rotundata. We used haploid males of the alfalfa leaf-cutting bee, M. rotundata, to overcome the limitation of the dominance of RAPD markers in the determination of population genetic parameters. Sixteen primers gave rise to 130 polymorphic and 31 monomorphic bands. The unbiased estimators calculated in this study include within- and between-population heterozygosity, nucleotide divergence, and genetic distance. The genetic diversity (H = 0.32–0.35) was found to be about 10 times that of previous estimates (H = 0.033) based on allozyme data. Contrary to the data obtained at the protein level, our results suggest that Hymenoptera do not have a lower level of genetic variability at the DNA level compared with other insect species. Regardless of the different assumptions underlying the calculation of heterozygosity, divergence, and genetic distance, all five populations showed a parallel interrelationship for the three parameters. We conclude that RAPD markers are a convenient tool to estimate population genetic variation in haploid M. rotundata and that with an adequate sample size the technique is applicable to the evaluation of divergence in diploid populations. Key words : Megachile rotundata, RAPD, heterozygosity, genetic distance, nucleotide divergence.

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