Genetic characterization of common carp (Cyprinus carpio) populations from Greece using mitochondrial DNA sequences

Biologia ◽  
2009 ◽  
Vol 64 (4) ◽  
Author(s):  
Anastasia Imsiridou ◽  
Alexandros Triantafyllidis ◽  
Athanasios Baxevanis ◽  
Costas Triantaphyllidis
Keyword(s):  
Mitochondrial Dna ◽  
Common Carp ◽  
Cyprinus Carpio ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Sequencing Analysis ◽  
Effective Population ◽  
Natural Habitats ◽  
D Loop ◽  
Population Sizes

AbstractWild common carp from two lakes and two rivers in Greece were genetically characterized with sequencing analysis of two mitochondrial DNA segments: cytochrome b (1119 bp) and D-loop (646 bp). A total of 9 variable singleton sites and 7 unique haplotypes were detected. A common haplotype was found in three out of the four populations examined, which seems to be the ancestral one and represents the European origin of common carp from Greece. This haplotype could be also justified by the introductions reported with individuals belonging to the Central European race, into many natural habitats in Greece. Limited genetic variation — in Evros and Aliakmonas populations — could be due to bottleneck effects and small effective population sizes, whereas the different haplotypes found in Lake Volvi could represent different common carp stocks. Values of sequence divergence among Greek haplotypes ranged from 0.0006 to 0.0023. The Neighbour-Joining (NJ) phylogenetic tree constructed based on the combined sequences, reveals that the populations of common carp from Greece belong to the European group of populations — which is highly divergent from the South East-Asia cluster — and to the subspecies Cyprinus carpio carpio.

scholarly journals Genetic Diversities and Historical Dynamics of Native Ethiopian Horse Populations (Equus caballus) Inferred from Mitochondrial DNA Polymorphisms

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 155
Author(s):  
Kefena Effa ◽  
Sonia Rosenbom ◽  
Jianlin Han ◽  
Tadelle Dessie ◽  
Albano Beja-Pereira
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Differentiation ◽  
Sequence Divergence ◽  
Dna Polymorphisms ◽  
Base Pairs ◽  
Feral Horses ◽  
Domestic Horses ◽  
D Loop ◽  
Diversity Estimates

Matrilineal genetic diversity and relationship were investigated among eight morphologically identified native Ethiopian horse populations using polymorphisms in 46 mtDNA D-loop sequences (454 base pairs). The horse populations identified were Abyssinian, Bale, Borana, Horro, Kafa, Kundido feral horses, Ogaden and Selale. Mitochondrial DNA D-loop sequences were characterized by 15 variable sites that defined five different haplotypes. All genetic diversity estimates, including Reynolds’ linearized genetic distance, genetic differentiation (FST) and nucleotide sequence divergence (DA), revealed a low genetic differentiation in native Ethiopian horse populations. However, Kundido feral and Borana domestic horses were slightly diverged from the rest of the Ethiopian horse populations. We also tried to shed some light on the matrilineal genetic root of native Ethiopian horses from a network constructed by combining newly generated haplotypes and reference haplotypes deposited in the GenBank for Eurasian type Turkish Anatolian horses that were used as a genetic conduit between Eurasian and African horse populations. Ninety-two haplotypes were generated from the combined Ethio-Eurasian mtDNA D-loop sequences. A network reconstructed from the combined haplotypes using Median-Joining algorithm showed that haplotypes generated from native Ethiopian horses formed separate clusters. The present result encourages further investigation of the genetic origin of native African horses by retrieving additional mtDNA sequences deposited in the GenBank for African and Eurasian type horses.

scholarly journals Large-Scale Hybridisation as an Extinction Threat to the Suweon Treefrog (Hylidae: Dryophytes suweonensis)

Animals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 764 ◽  
Author(s):  
Amaël Borzée ◽  
Jonathan J. Fong ◽  
Hoa Quynh Nguyen ◽  
Yikweon Jang
Keyword(s):  
Mitochondrial Dna ◽  
Species Distribution ◽  
Dna Sequences ◽  
Mass Extinction ◽  
Large Scale ◽  
Natural Habitats ◽  
Commensal Species ◽  
Polymorphic Microsatellites ◽  
Sixth Mass Extinction ◽  
Threaten Species

Amphibians are in the midst of a sixth mass extinction, and human activities play a major role in pushing species towards extinction. Landscape anthropisation has impacts that indirectly threaten species, in addition to the obvious destruction of natural habitats. For instance, land modification may bring human-commensal species in contact with sister-clades from which they were previously isolated. The species in these new contact zones are then able to hybridise to the point of reaching lineage fusion, through which the gene pool of the two species merges and one of the parental lineages becomes extirpated. Here, we documented the patterns of hybridisation between the spatially restricted D. suweonensis and the widespread D. japonicus. On the basis of the analysis of Cytochrome c oxidase subunit I mitochondrial DNA sequences (404 individuals from 35 sites) and six polymorphic microsatellites (381 individuals from 34 sites), we revealed a generalised, bi-directional, and geographically widespread hybridisation between the two species. Evidence of fertile back-crosses is provided by relatively high numbers of individuals in cyto-nuclear disequilibrium, as well as the presence of hybrid individuals further south than the species distribution limit, determined on the basis of call properties. Hybridisation is an additional threat to the endangered D. suweonensis.

Genetic diversity within Scorpio maurus (Scorpiones: Scorpionidae) from morocco: Preliminary evidence based on CO1 mitochondrial DNA sequences

Biologia ◽  
2008 ◽  
Vol 63 (6) ◽  
Author(s):  
Elsa Froufe ◽  
Pedro Sousa ◽  
Paulo Alves ◽  
David Harris
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Preliminary Analysis ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Preliminary Evidence ◽  
Evidence Based ◽  
Cytochrome Oxidase 1

AbstractThe large-clawed scorpion, Scorpio maurus, is a medically important scorpion and yet nothing is known regarding genetic diversity within this species. As a preliminary analysis we determined variation within the cytochrome oxidase 1 (CO1) mitochondrial gene from specimens from Morocco. High levels of genetic diversity were found that presented some geographical coherence. Of the two identified subspecies from Morocco, S. maurus birulai and S. maurus fuliginosus, the latter included genetically distinct lineages (8.0% uncorrected sequence divergence), indicating a detailed morphological and molecular revision is needed for this species.

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: A Correlation between the Effective and Census Population Sizes

2020 ◽  
Vol 12 (12) ◽  
pp. 2441-2449
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Range Size ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

Abstract What determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Because neutral diversity depends upon the product of the effective population size and mutation rate, there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here, we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest data set to date, using 639 mammalian species. In a multiple regression, we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of nonsynonymous to synonymous diversity, is also significantly negatively correlated to both range size and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12–20%, providing one of the first quantifications of the relationship between diversity and the census population size.

New DNA coalescent models and old population genetics software†

2016 ◽  
Vol 73 (9) ◽  
pp. 2178-2180 ◽  
Author(s):  
W. Stewart Grant ◽  
Einar Árnason ◽  
Bjarki Eldon
Keyword(s):  
Dna Sequences ◽  
Life Histories ◽  
Laboratory Data ◽  
Model Parameters ◽  
Effective Population ◽  
Coalescent Model ◽  
Null Distributions ◽  
Life History Pattern ◽  
Population Sizes ◽  
Software Programs

Abstract The analyses of often large amounts of field and laboratory data depend on computer programs to generate descriptive statistics and to test hypotheses. The algorithms in these programs are often complex and can be understood only with advanced training in mathematics and programming, topics that are beyond the capabilities of most fisheries biologists and empirical population geneticists. The backward looking Kingman coalescent model, based on the classic forward-looking Wright–Fisher model of genetic change, is used in many genetics software programs to generate null distributions against which to test hypotheses. An article in this issue by Niwa et al. shows that the assumption of bifurcations at nodes in the Kingman coalescent model is inappropriate for highly fecund Japanese sardines, which have type III life histories. Species with this life history pattern are better modelled with multiple mergers at the nodes of a coalescent gene genealogy. However, only a few software programs allow analysis with multiple-merger coalescent models. This parameter misspecification produces demographic reconstructions that reach too far into the past and greatly overestimates genetically effective population sizes (the number of individuals actually contributing to the next generation). The results of Niwa et al. underline the need to understand the assumptions and model parameters in the software programs used to analyse DNA sequences.

Genetic Structure of the Western and Eastern African Sahel/Savannah Belt and the Role of Nomadic Pastoralists as Inferred from the Variation of D-Loop Mitochondrial DNA Sequences

Human Biology ◽  
2017 ◽  
Vol 89 (4) ◽  
pp. 281 ◽  
Author(s):  
Martina Čížková ◽  
Pavel Munclinger ◽  
Mame Yoro Diallo ◽  
Iva Kulichová ◽  
Mohammed G. Mokhtar ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Nomadic Pastoralists ◽  
D Loop ◽  
African Sahel

scholarly journals Mitochondrial DNA Sequence Diversity in Mammals: a Correlation Between the Effective and Census Population Sizes

2020 ◽  
Author(s):  
Jennifer James ◽  
Adam Eyre-Walker
Keyword(s):  
Mitochondrial Dna ◽  
Metabolic Rate ◽  
Population Size ◽  
Effective Population Size ◽  
Dna Sequence ◽  
Sequence Diversity ◽  
Effective Population ◽  
Population Sizes ◽  
Census Population Size ◽  
The Relationship

AbstractWhat determines the level of genetic diversity of a species remains one of the enduring problems of population genetics. Since, neutral diversity depends upon the product of the effective population size and mutation rate there is an expectation that diversity should be correlated to measures of census population size. This correlation is often observed for nuclear but not for mitochondrial DNA. Here we revisit the question of whether mitochondrial DNA sequence diversity is correlated to census population size by compiling the largest dataset to date from 639 mammalian species. In a multiple regression we find that nucleotide diversity is significantly correlated to both range size and mass-specific metabolic rate, but not a variety of other factors. We also find that a measure of the effective population size, the ratio of non-synonymous to synonymous diversity, is also significantly negatively correlated to both range and mass-specific metabolic rate. These results together suggest that species with larger ranges have larger effective population sizes. The slope of the relationship between diversity and range is such that doubling the range increases diversity by 12 to 20%, providing one of the first quantifications of the relationship between effective and census population sizes.

scholarly journals Analysis of coyote mitochondrial DNA genotype frequencies: estimation of the effective number of alleles.

Genetics ◽  
1991 ◽  
Vol 128 (2) ◽  
pp. 405-416 ◽  
Author(s):  
N Lehman ◽  
R K Wayne
Keyword(s):  
Mitochondrial Dna ◽  
Geographic Location ◽  
Monte Carlo Sampling ◽  
Effective Population ◽  
Mobile Species ◽  
Genotype Frequencies ◽  
Site Survey ◽  
Population Sizes ◽  
High Gene ◽  
Mitochondrial Dna Genotype

Abstract A restriction-site survey of 327 coyotes (Canis latrans) from most parts of their North American range reveals 32 mitochondrial DNA (mtDNA) genotypes. The genotypes are not strongly partitioned in space, suggesting that there is high gene flow among coyote subpopulations. Consequently, each new geographic location added to the study has a decreasing probability of containing a mtDNA genotype that had not been previously discovered. This being the case, by using Monte Carlo sampling experiments, we can estimate the total number of genotypes that would be found if all possible localities were surveyed. This estimate of total genotypic variability agrees qualitatively with estimates based on theoretical considerations of the expected number of alleles in a stable population. We also predict effective population sizes from genotype data. The accuracy of these estimates is thought to be dependent on the fact that coyotes are not highly genetically structured, a situation which may apply to highly mobile species.

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