scholarly journals Patterns of Epigenetic Diversity in Two Sympatric Fish Species: Genetic vs. Environmental Determinants

Genes ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 107
Author(s):  
Laura Fargeot ◽  
Géraldine Loot ◽  
Jérôme G. Prunier ◽  
Olivier Rey ◽  
Charlotte Veyssière ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Fish Species ◽  
Genetic Background ◽  
Environmental Changes ◽  
Local Environment ◽  
Genetic Distances ◽  
Snp Markers ◽  
Epigenetic Variation ◽  
Wild Populations ◽  
Epigenetic Diversity

Epigenetic components are hypothesized to be sensitive to the environment, which should permit species to adapt to environmental changes. In wild populations, epigenetic variation should therefore be mainly driven by environmental variation. Here, we tested whether epigenetic variation (DNA methylation) observed in wild populations is related to their genetic background, and/or to the local environment. Focusing on two sympatric freshwater fish species (Gobio occitaniae and Phoxinus phoxinus), we tested the relationships between epigenetic differentiation, genetic differentiation (using microsatellite and single nucleotide polymorphism (SNP) markers), and environmental distances between sites. We identify positive relationships between pairwise genetic and epigenetic distances in both species. Moreover, epigenetic marks better discriminated populations than genetic markers, especially in G. occitaniae. In G. occitaniae, both pairwise epigenetic and genetic distances were significantly associated to environmental distances between sites. Nonetheless, when controlling for genetic differentiation, the link between epigenetic differentiation and environmental distances was not significant anymore, indicating a noncausal relationship. Our results suggest that fish epigenetic variation is mainly genetically determined and that the environment weakly contributed to epigenetic variation. We advocate the need to control for the genetic background of populations when inferring causal links between epigenetic variation and environmental heterogeneity in wild populations.

ELECTROPHORETIC VARIATION AND DIFFERENTIATION IN FOUR STRAINS OF DOMESTICATED RAINBOW TROUT (SALMO GAIRDNERI)

1979 ◽  
Vol 21 (1) ◽  
pp. 81-94 ◽  
Author(s):  
Craig A. Busack ◽  
Richard Halliburton ◽  
G. A. E. Gall
Keyword(s):  
Rainbow Trout ◽  
Genetic Variability ◽  
Genetic Differentiation ◽  
Balancing Selection ◽  
Genetic Distances ◽  
Salmo Gairdneri ◽  
Wild Populations ◽  
Electrophoretic Variation ◽  
High Level

A total of 1462 rainbow trout (Salmo gairdneri Richardson) representing four California domestic strains, were examined electrophoretically at 24 gene loci to investigate the amount of genetic variability within strains and genetic differentiation between strains, relative to wild populations. Estimated heterozygosities of 0.071 to 0.134 were similar to those reported for wild populations and thus indicated that the domestic strains were at least as variable as wild populations. Genetic distances between strains ranged from 0.011 to 0.067, values typical of the level of differentiation observed between local conspecific populations in a variety of organisms. It was suggested that this high level of heterozygosity is due to mixing of populations in the strains' histories and perhaps also to balancing selection.

scholarly journals Genetic diversity in global chicken breeds as a function of genetic distance to the wild populations

2020 ◽  
Author(s):  
Dorcus Kholofelo Malomane ◽  
Steffen Weigend ◽  
Armin Otto Schmitt ◽  
Annett Weigend ◽  
Christian Reimer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Founder Population ◽  
Wild Populations ◽  
Metabolic Processes ◽  
Evolutionary Forces ◽  
The Relationship

AbstractMigration of populations from their founder population is expected to cause a reduction in genetic diversity and facilitates population differentiation between the populations and their founder population as predicted by the theory of genetic isolation by distance. Consistent with that, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be well explained by their geographic expansion from the founders, which is correlated to the genetic differentiation. To investigate this in the chicken, we have estimated the relationship between the genetic diversity in 172 domesticated chicken populations and their genetic distances to wild populations. We have found a strong inverse relationship whereby 87.5% of the variation in the overall genetic diversity of domesticated chicken can be explained by the genetic distance to the wild populations. We also investigated if different types of SNPs and genes present similar patterns of genetic diversity as the overall genome. Among different SNP classes, the non-synonymous ones were the most deviating from the overall genome. However, the genetic distances to wild populations still explained more variation in domesticated chicken diversity in all SNP classes ranging from 81.7 to 88.7%. The genetic diversity seemed to change at a faster rate within the chicken in genes that are associated with transmembrane transport, protein transport and protein metabolic processes, and lipid metabolic processes. In general, such genes are flexible to be manipulated according to the population needs. On the other hand, genes which the genetic diversity hardly changes despite the genetic distance to the wild populations are associated with major functions e.g. brain development. Therefore, changes in the genes may be detrimental to the chickens. These results contribute to the knowledge of different evolutionary patterns of different functional genomic regions in the chicken.Author summaryThe chicken was first domesticated about 6000 B.C. in Asia from the jungle fowl. Following domestication, chickens were taken to different parts of the world mainly by humans. Evolutionary forces such as selection and genetic drift have shaped diversification within the chicken species. In addition, new breeds or strains have been developed from crossbreeding programs facilitated by man. These events, together with other breeding practices, have led to genomic alterations causing genetic differentiation between the domesticated chickens and their ancestral/wild population as well as manipulation of the genetic diversity within the domesticated chickens. We investigated the relationship between 172 domesticated chicken populations from different selection, breeding and management backgrounds and their genetic distance to the wild type chickens. We found that the genetic diversity within the populations decreases with the increasing genetic distances to the wild types. Human manipulation of chicken genetic diversity has more effect on the genetic differentiation than simple geographic separations (through migrations) do. We further found that some genes associated with vital functions show evolutionary constraints or persistent selection across the populations and do not comply with this relationship i.e. the genetic diversity within the populations is constant despite the change in the genetic distance to the wild types.

scholarly journals Reduced Global Genetic Differentiation of Exploited Marine Fish Species

2020 ◽  
Author(s):  
Miguel Gandra ◽  
Jorge Assis ◽  
Manuel Ramos Martins ◽  
David Abecasis
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Marine Fish ◽  
Fish Species ◽  
Population Differentiation ◽  
Environmental Changes ◽  
Meta Analysis ◽  
Genetic Connectivity

Abstract Knowledge on genetic structure is key to understand species connectivity patterns and to define the spatiotemporal scales over which conservation management plans should be designed and implemented. The distribution of genetic diversity (within and among populations) greatly influences species ability to cope and adapt to environmental changes, ultimately determining their long-term resilience to ecological disturbances. Yet, the drivers shaping connectivity and structure in marine fish populations remain elusive, as are the effects of fishing activities on genetic subdivision. To investigate these questions, we conducted a meta-analysis and compiled genetic differentiation data (FST/ΦST estimates) for more than 170 fish species from over 200 published studies globally distributed. We modeled the effects of multiple life-history traits, distance metrics, and methodological factors on observed population differentiation indices and specifically tested whether any signal arising from different exposure to fishing exploitation could be detected. Although the myriad of variables shaping genetic structure makes it challenging to isolate the influence of single drivers, results showed a significant correlation between commercial importance and genetic structure, with widespread lower population differentiation in commercially exploited species. Moreover, models indicate that variables commonly used as proxy for connectivity, such as larval pelagic duration, might be insufficient, and suggest that deep-sea species may disperse further. Overall, these results contribute to the growing body of knowledge on marine genetic connectivity and suggest a potential effect of commercial fisheries on the homogenization of genetic diversity, highlighting the need for additional research focused on dispersal ecology to ensure long-term sustainability of exploited marine species.

scholarly journals Genetic and Epigenetic Changes during the Upward Expansion of Deyeuxia angustifolia Kom. in the Alpine Tundra of the Changbai Mountains, China

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 291
Author(s):  
Biao Ni ◽  
Jian You ◽  
Jiangnan Li ◽  
Yingda Du ◽  
Wei Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Methylation ◽  
Genetic Variation ◽  
Soil Properties ◽  
Changbai Mountains ◽  
Epigenetic Variation ◽  
Geographical Distance ◽  
Mantel Tests ◽  
Epigenetic Diversity ◽  
Different Populations

Ecological adaptation plays an important role in the process of plant expansion, and genetics and epigenetics are important in the process of plant adaptation. In this study, genetic and epigenetic analyses and soil properties were performed on D. angustifolia of 17 populations, which were selected in the tundra zone on the western slope of the Changbai Mountains. Our results showed that the levels of genetic and epigenetic diversity of D. angustifolia were relatively low, and the main variation occurred among different populations (amplified fragment length polymorphism (AFLP): 95%, methylation sensitive amplification polymorphism (MSAP): 87%). In addition, DNA methylation levels varied from 23.36% to 35.70%. Principal component analysis (PCA) results showed that soil properties of different populations were heterogeneous. Correlation analyses showed that soil moisture, pH and total nitrogen were significantly correlated with genetic diversity of D. angustifolia, and soil temperature and pH were closely related to epigenetic diversity. Simple Mantel tests and partial Mantel tests showed that genetic variation significantly correlated with habitat or geographical distance. However, the correlation between epigenetic variation and habitat or geographical distance was not significant. Our results showed that, in the case of low genetic variation and genetic diversity, epigenetic variation and DNA methylation may provide a basis for the adaptation of D. angustifolia.

scholarly journals Genetic variability of marine shrimp in the Brazilian industry

2013 ◽  
Vol 48 (8) ◽  
pp. 968-974 ◽  
Author(s):  
Rodrigo Maggioni ◽  
Maria Raquel Moura Coimbra ◽  
Raimundo Bezerra da Costa ◽  
Fábio Mendonça Diniz ◽  
Wagner Franco Molina ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Central America ◽  
Microsatellite Loci ◽  
Geographical Location ◽  
Genetic Distances ◽  
Wild Populations ◽  
Marine Shrimp ◽  
Variability Level ◽  
Recent Origin ◽  
Polymorphic Microsatellite

The objective of this work was to estimate the genetic variability level and distribution in Brazilian broodstocks of marine shrimp (Litopenaeus vannamei). Nine of the country's largest hatcheries were evaluated using codominant and highly polymorphic microsatellite markers. The results obtained from genotyping of ten microsatellite loci are indicative of genetic variability that is compatible with that found in wild populations of L. vannamei in Mexico and Central America. A possible explanation is the highly diversified and relatively recent origin of the available broodstocks. Bayesian analysis detected a signal for five founding populations. The distribution of genetic distances partially reflects geographical location, and this information will be useful for the creation of new broodstocks. Therefore, L. vannamei genetic variability among nine of the largest national hatcheries can be considered high.

scholarly journals Clonal selection of Eucalyptus grandis x Eucalyptus globulus for productivity, adaptability, and stability, using SNP markers

2016 ◽  
Vol 65 (2) ◽  
pp. 30-38 ◽  
Author(s):  
D. Torres-Dini ◽  
A. C. P. Nunes ◽  
A. Aguiar ◽  
N. Nikichuk ◽  
C. Centurión ◽  
...  
Keyword(s):  
Eucalyptus Globulus ◽  
Environmental Changes ◽  
Clonal Selection ◽  
Eucalyptus Grandis ◽  
Small Population ◽  
Snp Markers ◽  
Hybrid Population ◽  
Environment Interaction ◽  
Predictive Capacity ◽  
Selection Of

Abstract In Uruguay, reforestations with Eucalyptus sp. is of fundamental importance to supply paper, pulp, and wood production. This study investigates genetic, productivity, stability, and adaptability parameters in the selection of Eucalypts grandis x Eucalyptus globulus full-sib hybrid clones. The study was conducted in a clonal test, repeated in two different soils types, in Rio Negro State, Uruguay. The population was characterized phenotypically for diameter at breast height (dbh) and genotyped for SNP markers (EuCHIP60K chip). Mean dbh was similar between sites and the genotype–environment interaction was simple. We found high genotype correlation in clone performance between environments (0.708), indicating the possibility of selecting the same clones for both study locations. Mean heritability between clones (0.724), coefficient of individual genetic variation (10.9 %), and relative variation (0.916), suggest the possibility of gains (estimated at 3.1 % for both sites together) by selecting clones with higher growth rates. A total of 15,196 SNPs were used to confirm parentage and test a genomic selection model for dbh. The predictive capacity was negative (-0.15) given the small population size (78 individuals). The most adaptable material among the tested study sites presented higher values for SNP heterozygosity. Thus, using molecular markers to identify clones responsive to environmental changes can act as a powerful tool in Eucalyptus breeding programs. The hybrid population showed greater adaptability than E. globulus for this region.

scholarly journals Effect of land-use types on the ecomorphological structure of fish assemblage in distinct mesohabitats of neotropical streams

2021 ◽  
Vol 21 (3) ◽  
Author(s):  
Leonardo Antunes Pessoa ◽  
Matheus Tenório Baumgartner ◽  
Marcelo Percilio Santana Junior ◽  
João Paulo Alves Pagotto ◽  
Luiz Gustavo Antunes Pessoa ◽  
...  
Keyword(s):  
Land Use ◽  
Urban Environment ◽  
Fish Species ◽  
Fish Assemblage ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Canopy Cover ◽  
Distinct Species ◽  
Urban Streams ◽  
Land Use Types

Abstract The use and occupation of land by human population substantially influence environmental variables and fish assemblage in streams. However, there is little knowledge on how these changes affect the ecomorphological structure of fish assemblage in mesohabitats. Therefore, we aim to assess whether the land-use types affect the ecomorphological structure of fish assemblage in distinct mesohabitats. Environmental and ichthyofaunistic data were collected in three mesohabitats (rifles, runs, and pools) of five rural and five urban streams. Twenty-one ecomorphological indices were obtained from the mean of linear morphological measurements and areas of the fishes. Subsequently, the Euclidean distance was calculated, based on the ecomorphological indices, between each pair of species, to measure the ecomorphological distances for the mesohabitats of the rural and urban streams. The results show that the urban environment is more harmful to streams than the rural one, due to changes in the environmental variables and decrease in species richness. The main environmental changes found in urban streams were the decrease in canopy cover by riparian vegetation and dissolved oxygen, and the increase in electrical conductivity and bed silting. Also, there was a significant decrease in the morphological similarity between fish species in the mesohabitats of urban streams compared to rural ones. Therefore, we can conclude that the urban environment leads to the loss of morphologically similar fish species in the mesohabitats, with only a few functionally distinct species remaining.

scholarly journals BIOCHEMICAL GENETIC DIFFERENTIATION AMONG WILD POPULATIONS OF MILKFISH (Chanos chanos) IN INDONESIA

2017 ◽  
Vol 4 (1) ◽  
pp. 11
Author(s):  
Ketut Sugama ◽  
Agus Prijono
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Coastal Water ◽  
Wild Populations ◽  
Chanos Chanos ◽  
South Sulawesi ◽  
Biochemical Genetic

Four populations of milkfish (Chanos chanos ) were collected (N=100) from coastal water of  Aceh. Bali, East Java and South Sulawesi and were examined electrophoretically at 29 loci to deterurine the genetic vuriability and the population structure.

scholarly journals Genetic diversity and population structure among goat genotypes in Kenya

2020 ◽  
Author(s):  
Ruth W. Waineina ◽  
Kiplangat Ngeno ◽  
Tobias O. Otieno ◽  
Evans D. Ilatsia
Keyword(s):  
Population Structure ◽  
Principal Component ◽  
Genetic Distances ◽  
Snp Markers ◽  
Founder Population ◽  
Good Opportunity ◽  
Model Based Clustering ◽  
Population Structuring ◽  
Improvement Programs ◽  
Genotype Clustering

AbstractPopulation structure and relationship information among goats is critical for genetic improvement, utilization and conservation. This study explored population structure and level of gene intermixing among four goat genotypes in Kenya: Alpine (n = 30), Toggenburg (n = 28), Saanen (n = 24) and Galla (n = 12). The population structuring and relatedness were estimated using principal component analysis utilizing allele frequencies of the SNP markers. Genotype relationships were evaluated based on the calculated Reynolds genetic distances. A phylogenetic tree was constructed to represent genotype clustering using iTOL software. Population structure was investigated using model-based clustering (ADMIXTURE) Genotypes relationships revealed four distinctive clusters: Alpine, Galla, Saanen and Toggenburg. The ADMIXTURE results revealed some level of gene intermixing among Alpine, Toggenburg and Saanen with Galla. Saanen goats were the most admixed genotype with 84%, 7% and 4% of its genome derived from Galla, Alpine and Toggenburg respectively. Alpine and Toggenburg goats shared some associations with the Galla goat; 10% and 1% respectively. The association of Galla with other genotypes was anticipated since Galla goat was used as the founder population for crossbreeding with Saanen, Alpine and Toggenburg breed. The genetic variations among the goat genotypes observed, will provide a good opportunity for sustainable utilization, conservation and future genetic resource improvement programs in goat genotypes in Kenya.

scholarly journals A review of length-weight relationships of freshwater fishes in Malaysia

2018 ◽  
Vol 20 (1) ◽  
pp. 55-68 ◽  
Author(s):  
Amonodin Mohamad Radhi ◽  
Mohd-Fadzil Nurul Fazlinda ◽  
Mohammad Noor Azmai Amal ◽  
Hashim Rohasliney
Keyword(s):  
Freshwater Fish ◽  
Fish Species ◽  
Environmental Changes ◽  
Meta Analysis ◽  
Freshwater Fishes ◽  
Clarias Batrachus ◽  
Ecological Health ◽  
Allometric Growth ◽  
Freshwater Fish Species

Abstract This manuscript reviews the length-weight relationships (LWRs) of freshwater fishes in Malaysia. A total of 102 LWRs of fishes gathered from literature pertaining to 64 freshwater fish species were analysed. A meta-analysis from 13 previous reports showed that the b values was ranged from 2.19 (Clarias batrachus) to 4.106 (Barbodes binotatus). Out of 64 observed species, 47 species (11 families) experienced positive allometric growth, while another 23 species (eight families) and 31 species (12 families) were recorded under isometric and negative allometric growth, respectively. The fish LWRs observed can be used as an indicator of environmental changes and fish ecological health for freshwater fishes in Malaysia.

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