scholarly journals Unraveling the Limits of Mitochondrial Control Region to Estimate the Fine Scale Population Genetic Differentiation in Anadromous FishTenualosa ilisha

Scientifica ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Rashmi Verma ◽  
Mahender Singh ◽  
Sudhir Kumar
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Control Region ◽  
Population Genetic ◽  
Arabian Sea ◽  
Mitochondrial Control Region ◽  
Population Genetic Differentiation ◽  
First Choice ◽  
Scale Population ◽  
And Control

The mitochondrial control region has been the first choice for examining the population structure but hypervariability and homoplasy have reduced its suitability. We analysed eight populations using control region for examining the population structure ofHilsa. Although the control region analysis revealed broad structuring between the Arabian Sea and Bay of Bengal (FST  0.0441,p<0.001) it was unable to detect structure among riverine populations. These results suggest that the markers used must be able to distinguish populations and control region has led to an underestimation of genetic differentiation among populations ofHilsa.

Postglacial population genetic differentiation potentially facilitated by a flexible migratory strategy in Golden-crowned Kinglets (Regulussatrapa)

2014 ◽  
Vol 92 (2) ◽  
pp. 163-172 ◽  
Author(s):  
T.M. Burg ◽  
S.A. Taylor ◽  
K.D. Lemmen ◽  
A.J. Gaston ◽  
V.L. Friesen
Keyword(s):  
Genetic Differentiation ◽  
Population Genetic ◽  
Ice Sheets ◽  
Mitochondrial Control Region ◽  
Ice Age ◽  
Haida Gwaii ◽  
Population Genetic Differentiation ◽  
Queen Charlotte Islands ◽  
Base Pair Fragment ◽  
Migratory Strategy

Relatively recently, temperate regions in North America were covered by extensive ice sheets, making them inhospitable to contemporary flora and fauna. Since the retreat of the ice sheets, these regions have been recolonized by a diversity of taxa, some of which have undergone rapid postglacial divergence. Evidence supports the hypothesis that some taxa persisted in unglaciated refugia during the Last Glacial Maximum, such as on Haida Gwaii (formerly the Queen Charlotte Islands). Many taxa on Haida Gwaii are genetically distinct from mainland populations at neutral molecular markers possibly as the result of isolation in refugia or postglacial colonization. The Golden-crowned Kinglet (Regulus satrapa Lichtenstein, 1823) is a continentally distributed, short-distance migratory passerine inhabiting mature conifer forests including those on Haida Gwaii. We used five microsatellite markers and a 568 base-pair fragment of the mitochondrial control region to determine the likelihood that Haida Gwaii region acted as a refugium for this species during the last ice age. We report significant gene flow between Haida Gwaii and the western North American mainland from mitochondrial markers, but significant population genetic differentiation at nuclear markers. We also report genetic divergence between eastern and western Golden-crowned Kinglets, as well as higher genetic diversity and population substructuring within the western population than within the eastern population. The east–west differentiation probably arose due to isolation in separate Pleistocene refugia south of the ice sheets. However, population differences within the west are likely caused by more recent processes; contemporary differentiation of Haida Gwaii Golden-crowned Kinglets most likely occurred postglacially.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Geography is more important than life history in the recent diversification of the tiger salamander complex

2021 ◽  
Vol 118 (17) ◽  
pp. e2014719118
Author(s):  
Kathryn M. Everson ◽  
Levi N. Gray ◽  
Angela G. Jones ◽  
Nicolette M. Lawrence ◽  
Mary E. Foley ◽  
...  
Keyword(s):  
Life History ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Tiger Salamander ◽  
Life History Variation ◽  
Mexican Axolotl ◽  
Population Genetic Differentiation ◽  
Wide Range ◽  
Lineage Divergence

The North American tiger salamander species complex, including its best-known species, the Mexican axolotl, has long been a source of biological fascination. The complex exhibits a wide range of variation in developmental life history strategies, including populations and individuals that undergo metamorphosis; those able to forego metamorphosis and retain a larval, aquatic lifestyle (i.e., paedomorphosis); and those that do both. The evolution of a paedomorphic life history state is thought to lead to increased population genetic differentiation and ultimately reproductive isolation and speciation, but the degree to which it has shaped population- and species-level divergence is poorly understood. Using a large multilocus dataset from hundreds of samples across North America, we identified genetic clusters across the geographic range of the tiger salamander complex. These clusters often contain a mixture of paedomorphic and metamorphic taxa, indicating that geographic isolation has played a larger role in lineage divergence than paedomorphosis in this system. This conclusion is bolstered by geography-informed analyses indicating no effect of life history strategy on population genetic differentiation and by model-based population genetic analyses demonstrating gene flow between adjacent metamorphic and paedomorphic populations. This fine-scale genetic perspective on life history variation establishes a framework for understanding how plasticity, local adaptation, and gene flow contribute to lineage divergence. Many members of the tiger salamander complex are endangered, and the Mexican axolotl is an important model system in regenerative and biomedical research. Our results chart a course for more informed use of these taxa in experimental, ecological, and conservation research.

scholarly journals Genetic Diversity in the mtDNA control region and population structure of Chrysichthys nigrodigitatus from selected Nigerian rivers: Implications for conservation and aquaculture

2016 ◽  
Vol 24 (2) ◽  
pp. 85-97 ◽  
Author(s):  
Sylvanus A. Nwafili ◽  
Tian-Xiang Gao
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Control Region ◽  
Haplotype Diversity ◽  
Population Expansion ◽  
Mitochondrial Control Region ◽  
Recent Population Expansion ◽  
Base Pair Fragment ◽  
Population Structures ◽  
High Level

Abstract The genetic diversity and population structure of Chrysichthys nigrodigitatus were evaluated using a 443 base pair fragment of the mitochondrial control region. Among the eight populations collected comprising 129 individuals, a total of 89 polymorphic sites defined 57 distinct haplotypes. The mean haplotype diversity and nucleotide diversity of the eight populations were 0.966±0.006 and 0.0359±0.004, respectively. Analysis of molecular variance showed significant genetic differentiation among the eight populations (FST =0.34; P < 0.01). The present results revealed that C. nigrodigitatus populations had a high level of genetic diversity and distinct population structures. We report the existence of two monophyletic matrilineal lineages with mean genetic distance of 10.5% between them. Non-significant negative Tajima’s D and Fu’s Fs for more than half the populations suggests that the wild populations of C. nigrodigitatus underwent a recent population expansion, although a weak one since the late Pleistocene.

Evidence supporting panmixia in Greenland halibut (Reinhardtius hippoglossoides) in the Northwest Atlantic

2014 ◽  
Vol 71 (5) ◽  
pp. 763-774 ◽  
Author(s):  
Denis Roy ◽  
David C. Hardie ◽  
Margaret A. Treble ◽  
James D. Reist ◽  
Daniel E. Ruzzante
Keyword(s):  
Population Structure ◽  
Population Genetic ◽  
Conservation Strategies ◽  
Greenland Halibut ◽  
Northwest Atlantic ◽  
Population Genetic Differentiation ◽  
Conservation Implications ◽  
Greenland Halibut Reinhardtius Hippoglossoides ◽  
Reinhardtius Hippoglossoides ◽  
Species Specific

Assessment of population structure is critical to the design and implementation of sound management and conservation strategies. However, population structure must be assessed using markers attuned to population genetic processes such as genetic drift and gene flow, which reflect actual levels of reproductive isolation among putative genetic clusters. This is critical for highly exploited, commercial species that form the backbone of regional and local economies. Here, we show extremely low levels of population genetic differentiation among Greenland halibut (Reinhardtius hippoglossoides) collected from throughout the Northwest Atlantic, which cannot be statistically differentiated from panmixia using 12 species-specific polymorphic microsatellite markers. In contrast, some previous studies have demonstrated significant differences among individuals collected from various parts of the species’ range using a variety of both genetic and nongenetic techniques. In accordance with other reports and consistent with the species’ life history, we demonstrate that the most parsimonious explanation reconciling observed patterns is a repeated high degree of local differentiation of new recruits and colonizers originating from a common gene pool. Such a scenario has important conservation implications in terms of devising more appropriate strategies balancing species persistence and replenishment with sustainable resource use.

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