Genetic-Variation Among Insular Populations of the Sleepy Lizard, Trachydosaurus-Rugosus Gray (Squamata, Scincidae)

1990 ◽  
Vol 38 (6) ◽  
pp. 603 ◽  
Author(s):  
S Sarre ◽  
TD Schwaner ◽  
A Georges
Keyword(s):  
Genetic Variation ◽  
Genetic Drift ◽  
Allelic Diversity ◽  
South Australia ◽  
Allozyme Electrophoresis ◽  
Specific Component ◽  
Genetic Characteristics ◽  
Island Populations ◽  
Evolutionary Forces ◽  
Insular Populations

Seven island populations of the sleepy lizard, Trachydosaurus rugosus, in South Australia were studied to establish the genetic effects of isolation. These effects were assessed by comparing genetic characteristics (using allozyme electrophoresis) of the island populations with those of three adjacent mainland populations. Heterozygosity levels did not vary significantly among the populations although the island populations exhibited reduced allelic diversity. Alleles that were rare on the mainland were not present in the island populations. Genetic divergence among the island populations was much greater than among populations on the mainland, reinforcing the notion that evolutionary forces, probably genetic drift, were greatest among the insular populations. This study demonstrates that the intra-specific component of variation can be significant, and that the importance of this component will increase with the fragmentation and isolation of populations. This finding serves to emphasis the importance of considering the population as the unit of conservation.

scholarly journals Detecting selection from linked sites using an F-model

2019 ◽  
Author(s):  
Marco Galimberti ◽  
Christoph Leuenberger ◽  
Beat Wolf ◽  
Sándor Miklós Szilágyi ◽  
Matthieu Foll ◽  
...  
Keyword(s):  
Markov Model ◽  
Human Genome ◽  
Genetic Drift ◽  
Statistical Power ◽  
Hidden Markov ◽  
Allele Frequencies ◽  
Human Genome Diversity Project ◽  
Genome Diversity ◽  
Specific Component ◽  
Evolutionary Forces

ABSTRACTAllele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allele frequency differences among populations connected by migration is the F-model, which measures differences in allele frequencies by population specific FST coefficients. This model readily accounts for multiple evolutionary forces by partitioning FST coefficients into locus and population specific components reflecting selection and drift, respectively. Here we present an extension of this model to linked loci by means of a hidden Markov model (HMM) that characterizes the effect of selection on linked markers through correlations in the locus specific component along the genome. Using extensive simulations we show that our method has up to two-fold the statistical power of previous implementations that assume sites to be independent. We finally evidence selection in the human genome by applying our method to data from the Human Genome Diversity Project (HGDP).

Morphological Variation and Fluctuating Asymmetry Among Insular Populations of the Sleepy Lizard, Trachydosaurus-Rugosus Gray (Squamata, Scincidae)

1991 ◽  
Vol 39 (1) ◽  
pp. 91 ◽  
Author(s):  
S Sarre ◽  
JM Dearn
Keyword(s):  
Fluctuating Asymmetry ◽  
Morphological Characteristics ◽  
South Australia ◽  
Morphological Characters ◽  
Small Population ◽  
Developmental Stability ◽  
Developmental Instability ◽  
Allozyme Electrophoresis ◽  
Genetic Changes ◽  
Island Populations

Morphological characteristics of island populations of the sleepy lizard, Trachydosaurus rugosus, were compared with those of three adjacent mainland populations in South Australia. An analysis of 21 morphological characters revealed greater divergence among the island populations than among those on the mainland. However, in contrast with the findings of an earlier study using allozyme electrophoresis, morphological relationships among populations showed little congruence with the relationships expected from their geographic proximity. Two measures of developmental stability (fluctuating asymmetry and percentage gross abnormalities) varied significantly among the populations. High levels of developmental instability were observed in three of the island populations. It is not possible to rule out environmental causes of the increased developmental instability but it appears more likely that it is caused by genetic drift and inbreeding resulting from small population size. These results suggest that developmental stability may be more useful in monitoring genetic changes in wildlife populations than the conventional method of allozyme electrophoresis.

scholarly journals Detecting Selection from Linked Sites Using an F-Model

Genetics ◽  
2020 ◽  
Vol 216 (4) ◽  
pp. 1205-1215
Author(s):  
Marco Galimberti ◽  
Christoph Leuenberger ◽  
Beat Wolf ◽  
Sándor Miklós Szilágyi ◽  
Matthieu Foll ◽  
...  
Keyword(s):  
Markov Model ◽  
Human Genome ◽  
Genetic Drift ◽  
Statistical Power ◽  
Hidden Markov ◽  
Allele Frequencies ◽  
Human Genome Diversity Project ◽  
Genome Diversity ◽  
Specific Component ◽  
Evolutionary Forces

Allele frequencies vary across populations and loci, even in the presence of migration. While most differences may be due to genetic drift, divergent selection will further increase differentiation at some loci. Identifying those is key in studying local adaptation, but remains statistically challenging. A particularly elegant way to describe allele frequency differences among populations connected by migration is the F-model, which measures differences in allele frequencies by population specific FST coefficients. This model readily accounts for multiple evolutionary forces by partitioning FST coefficients into locus- and population-specific components reflecting selection and drift, respectively. Here we present an extension of this model to linked loci by means of a hidden Markov model (HMM), which characterizes the effect of selection on linked markers through correlations in the locus specific component along the genome. Using extensive simulations, we show that the statistical power of our method is up to twofold higher than that of previous implementations that assume sites to be independent. We finally evidence selection in the human genome by applying our method to data from the Human Genome Diversity Project (HGDP).

Genetic variation in allozymes of western larch

1986 ◽  
Vol 16 (5) ◽  
pp. 1013-1018 ◽  
Author(s):  
Lauren Fins ◽  
Lisa W. Seeb
Keyword(s):  
Genetic Variation ◽  
Genetic Drift ◽  
Fire History ◽  
Glacial History ◽  
Geographic Proximity ◽  
Electrophoretic Variation ◽  
Inland Empire ◽  
Genetic History ◽  
Expected Heterozygosity ◽  
History Of

Seed samples from 19 stands of Larixoccidentalis Nutt. were analyzed for electrophoretic variation at 23 loci. Because sample sizes consisted of only 9 or 10 trees per stand (18–20 alleles per locus per stand), samples were grouped by geographic proximity into four larger samples. For all measures of variation, this species scored lower than most, but within the range observed for other western conifers. Most of the variation was found within rather than between the population groups. The single southern sample appeared to be genetically distinct from the others. Although some variation was observed between individual stand samples in expected heterozygosity, the consistently low values for all samples suggest that genetic drift has played a major role in the genetic history of the species in the Inland Empire, both through its glacial history in postulated refugia and through fire history in recent times.

scholarly journals Taxonomic status of two morphotypes of Coryphaena hippurus (Perciformes: Coryphaenidae)

2017 ◽  
Vol 15 (1) ◽  
Author(s):  
Alan Bonner ◽  
Michelle R. Duarte ◽  
Rosa C. C. L. Souza ◽  
Cassiano Monteiro-Neto ◽  
Edson P. Silva
Keyword(s):  
Genetic Variation ◽  
Taxonomic Status ◽  
Brazilian Coast ◽  
Gene Pools ◽  
Fishing Pressure ◽  
Allozyme Electrophoresis ◽  
Coryphaena Hippurus ◽  
Biological Matter ◽  
Electrophoresis Method ◽  
Definition Of

ABSTRACT Two Coryphaena hippurus morphotypes (dourado and palombeta) are found along the Brazilian coast and are considered by Rio de Janeiro’s fisherman and fishmongers as two different species. Furthermore, these morphotypes are commercialized under different values and suffer different fishing pressure. Therefore, a definition of their taxonomic status is an important economic and biological matter. In order to investigate this problem, allozyme electrophoresis method was undertaken for seventeen loci on 117 individuals of C. hippurus sampled at Cabo Frio/RJ (Brazil). The data indicate homogeneity between the morphotypes gene pools. Nevertheless, differences were found for genetic variation among dourado and palombeta, especially due to alcohol dehydrogenase locus. Natural selection hypothesis is discussed in explaining these findings.

scholarly journals Genomic and demographic processes differentially influence genetic variation across the X chromosome

2021 ◽  
Author(s):  
Daniel J. Cotter ◽  
Timothy H. Webster ◽  
Melissa A. Wilson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
X Chromosome ◽  
Global Scale ◽  
Careful Consideration ◽  
Human Populations ◽  
Evolutionary Forces ◽  
Ideal System ◽  
Demographic Patterns

AbstractMutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

scholarly journals Genetic variation in dispersal plasticity in an aquatic host-parasite model system

2020 ◽  
Author(s):  
Giacomo Zilio ◽  
Louise Solveig Noergaard ◽  
Giovanni Petrucci ◽  
Nathalie Zeballos ◽  
Claire Gougat-Barbera ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Internal State ◽  
Theoretical Models ◽  
Infection Prevalence ◽  
Main Role ◽  
Dependent Plasticity ◽  
Evolutionary Forces ◽  
State Dependent ◽  
Context Dependent ◽  
Host Parasite

Dispersal plays a main role in determining spatial dynamics, and both theory and empirical evidence indicate that evolutionary optima exist for constitutive or plastic dispersal behaviour. Plasticity in dispersal can be influenced by factors both internal (state-dependent) or external (context-dependent) to individuals. Parasitism is interesting in this context, as it can influence both types of host dispersal plasticity: individuals can disperse in response to internal infection status but might also respond to the presence of infected individuals around them. We still know little about the driving evolutionary forces of host dispersal plasticity, but a first requirement is the presence of a genetic basis on which natural selection can act. In this study, we used microcosm dispersal mazes to investigate plastic dispersal of 20 strains of the freshwater protist Paramecium caudatum in response to the bacterial parasite Holospora undulata. We additionally quantified the genetic component of the plastic responses, i.e. the heritability of state- and context-depended dispersal. We found that infection by the parasite can either increase or decrease dispersal of individual strains relative to the uninfected (state-dependent plasticity), and this to be heritable. We also found strain-specific change of dispersal of uninfected Paramecium when exposed to variable infection prevalence (context-dependent plasticity) with very low level of heritability. To our knowledge, this is the first explicit empirical demonstration and quantification of genetic variation of plastic dispersal in a host-parasite system, which could have important implications for meta-population and epidemiological dynamics. We discuss some of the underlying mechanisms of this variation and link our results to the existing theoretical models.

scholarly journals Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247586
Author(s):  
Christine E. Edwards ◽  
Brooke C. Tessier ◽  
Joel F. Swift ◽  
Burgund Bassüner ◽  
Alexander G. Linan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Plant Species ◽  
Genetic Drift ◽  
Rare Species ◽  
Ex Situ ◽  
Ouachita Mountains ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

scholarly journals Evolution of gene regulatory networks by means of selection and random genetic drift

2018 ◽  
Author(s):  
Antonios Kioukis ◽  
Pavlos Pavlidis
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Genetic Drift ◽  
Regulatory Networks ◽  
Fitness Landscape ◽  
Random Genetic Drift ◽  
Maturation Period ◽  
Evolutionary Forces ◽  
Gene Regulatory

The evolution of a population by means of genetic drift and natural selection operating on a gene regulatory network (GRN) of an individual has not been scrutinized in depth. Thus, the relative importance of various evolutionary forces and processes on shaping genetic variability in GRNs is understudied. Furthermore, it is not known if existing tools that identify recent and strong positive selection from genomic sequences, in simple models of evolution, can detect recent positive selection when it operates on GRNs. Here, we propose a simulation framework, called EvoNET, that simulates forward-in-time the evolution of GRNs in a population. Since the population size is finite, random genetic drift is explicitly applied. The fitness of a mutation is not constant, but we evaluate the fitness of each individual by measuring its genetic distance from an optimal genotype. Mutations and recombination may take place from generation to generation, modifying the genotypic composition of the population. Each individual goes through a maturation period, where its GRN reaches equilibrium. At the next step, individuals compete to produce the next generation. As time progresses, the beneficial genotypes push the population higher in the fitness landscape. We examine properties of the GRN evolution such as robustness against the deleterious effect of mutations and the role of genetic drift. We confirm classical results from Andreas Wagner’s work that GRNs show robustness against mutations and we provide new results regarding the interplay between random genetic drift and natural selection.

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