scholarly journals Development of microsatellite loci and population genetics of the catfish Pimelodus yuma (Siluriformes: Pimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Cristhian Danilo Joya ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
Lower Section ◽  
Habitat Disturbances ◽  
Genetic Groups ◽  
Lack Of Information ◽  
Species Specific

ABSTRACT Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.

scholarly journals Microsatellite loci development and population genetics in Neotropical fish Curimata mivartii (Characiformes: Curimatidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5959 ◽  
Author(s):  
Ricardo M. Landínez-García ◽  
Edna J. Marquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Molecular Tools ◽  
Migratory Species ◽  
Lower Section ◽  
Neotropical Fish ◽  
International Union ◽  
Commercially Important ◽  
Species Specific ◽  
Near Threatened

The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae.

scholarly journals Range-Wide and Regional Patterns of Population Structure and Genetic Diversity in the Gopher Tortoise

2017 ◽  
Vol 8 (2) ◽  
pp. 497-512 ◽  
Author(s):  
D. Gaillard ◽  
J.R. Ennen ◽  
B.R. Kreiser ◽  
C.P. Qualls ◽  
S.C. Sweat ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Microsatellite Loci ◽  
Spatial Scales ◽  
Demographic History ◽  
Genetic Admixture ◽  
Gopher Tortoise ◽  
Regional Patterns ◽  
Genetic Groups

Abstract The gopher tortoise (Gopherus polyphemus) has experienced dramatic population declines throughout its distribution in the southeastern United States and is federally listed as threatened in the area west of the Tombigbee and Mobile rivers. While there is molecular support for recognizing the listed portion of the range as genetically distinct, other research has suggested that additional population structure exists at both range-wide and regional scales. In this study, we sought to comprehensively define genetic population structure at both spatial scales by doubling the data available in terms of the number of sampling sites, individuals, and microsatellite loci compared to previously published work. We also compared patterns of genetic diversity, gene flow, and demographic history across the range. We collected 933 individuals from 47 sampling sites across the range and genotyped them for 20 microsatellite loci. Our range-wide analyses supported the recognition of five genetic groups (or regions) delineated by the Tombigbee and Mobile rivers, Apalachicola and Chattahoochee rivers, and the transitional areas between several physiographic province sections of the Coastal Plains (i.e., Eastern Gulf, Sea Island, and Floridian). We found genetic admixture at sampling sites along the boundaries of these genetically defined groups. We detected some degree of additional genetic structure within each of the five regions. Notably, within the range listed as threatened under the Endangered Species Act, we found some support for two additional genetic groups loosely delineated by the Pascagoula and Chickasawhay rivers, and we detected four more genetic groups within the Florida region that seemed to reflect the influence of the local physiography. Additionally, our range-wide analysis found the periphery of the range had lower levels of genetic diversity relative to the core. We suggest that the five main genetic groups delineated in our study warrant recognition as management units in terms of conservation planning. Intraregional population structure also points to the potential importance of other barriers to gene flow at finer spatial scales, although additional work is needed to better delineate these genetic groups.

scholarly journals Characterizing the genetic diversity of the Andean blueberry (Vaccinium floribundum Kunth.) across the Ecuadorian Highlands

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243420
Author(s):  
Pamela Vega-Polo ◽  
Maria Mercedes Cobo ◽  
Andrea Argudo ◽  
Bernardo Gutierrez ◽  
Jennifer Rowntree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Anthropogenic Activities ◽  
Conservation Status ◽  
Ecological Factors ◽  
Andean Region ◽  
Key Factor ◽  
Species Specific

The Ecuadorian páramo, a high altitude tundra-like ecosystem, is a unique source of various ecosystem services and distinct biodiversity. Anthropogenic activities are associated with its fragmentation, which alters ecological factors and directly threatens resident species. Vaccinium floribundum Kunth., commonly known as Andean blueberry or mortiño, is a wild shrub endemic to the Andean region and highly valued in Ecuador for its berries, which are widely used in food preparations and hold an important cultural value. Since it is a wild species, mortiño could be vulnerable to environmental changes, resulting in a reduction of the size and distribution of its populations. To evaluate the extent of these effects on the mortiño populations, we assessed the genetic diversity and population structure of the species along the Ecuadorian highlands. We designed and developed a set of 30 species-specific SSR (simple sequence repeats) markers and used 16 of these to characterize 100 mortiño individuals from 27 collection sites. Our results revealed a high degree of genetic diversity (HE = 0.73) for the Ecuadorian mortiño, and a population structure analyses suggested the existence of distinct genetic clusters present in the northern, central and southern highlands. A fourth, clearly differentiated cluster was also found and included individuals from locations at higher elevations. We suggest that the population structure of the species could be explained by an isolation-by-distance model and can be associated with the geological history of the Andean region. Our results suggest that elevation could also be a key factor in the differentiation of mortiño populations. This study provides an extensive overview of the species across its distribution range in Ecuador, contributing to a better understanding of its conservation status. These results can assist in the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystem as a whole.

scholarly journals Population genetics of three threatened catfish species in heterogeneous environments of the Cauca River, Colombia

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Natalia Restrepo-Escobar ◽  
Anny Johanna Yepes-Acevedo ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Decision Making ◽  
Population Genetics ◽  
Fish Populations ◽  
Heterogeneous Environments ◽  
Threatened Fish ◽  
Hydroelectric Development ◽  
Genetic Groups ◽  
Management Plans ◽  
Species Specific

ABSTRACT Neotropical catfishes Ageneiosus pardalis, Pimelodus grosskopfii and Sorubim cuspicaudus are migratory fishes of commercial importance that exhibit decreasing populations due to overfishing and other anthropic interventions. This study used species-specific microsatellite loci to test the hypothesis that threatened fish populations show genetic vulnerability signs and are genetically structured in the middle and lower sections of the Cauca River. The studied species exhibit genetic diversity levels higher than the average values reported for Neotropical Siluriformes; however, they seem to have suffered recent bottlenecks and they present significant endogamy levels that are higher for the critically endangered catfish P. grosskopfii. Furthermore, both Ageneiosus pardalis and S. cuspicaudus are each formed by one genetic group, while Pimelodus grosskopfii comprises two coexisting genetic groups. The information obtained in this study is useful for the decision making in management plans that are appropriate for the sustainability of these three species populations within the proposal for the expansion of the hydroelectric development and other anthropic activities.

scholarly journals Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Kevin León García-Castro ◽  
José David Rangel-Medrano ◽  
Ricardo Marcel Landínez-García ◽  
Edna Judith Márquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Anthropogenic Activities ◽  
South American ◽  
Important Species ◽  
Large Size ◽  
Genetic Diversity And Structure ◽  
Commercially Important ◽  
Species Specific ◽  
Generation Sequencing

ABSTRACT The Neotropical catfish genus Pseudoplatystoma comprises eight species of large size, widely distributed in South American basins. The endangered species P. magdaleniatum is endemic to Magdalena basin (Colombia), experiences high fishing pressure and its population genetics is relatively unknown. To study the genetic status and structure of P. magdaleniatum, 25 species-specific polymorphic microsatellite loci were developed using next-generation sequencing and then tested in samples collected in the Magdalena-Cauca basin. Based on 15 of these loci, P. magdaleniatum showed a high number of alleles per locus (9-10), high values of observed (0.762-0.798) and expected (0.770-0.791) heterozygosities, recent reduction of population size and gene flow. These findings constitute a baseline to measure potential changes in genetic diversity and structure of this commercially important species in a basin undergoing high anthropogenic activities.

scholarly journals Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
José David Rangel-Medrano ◽  
Edna Judith Márquez
Keyword(s):  
Genetic Diversity ◽  
Population Genetics ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Microsatellite Loci ◽  
Population Genetic ◽  
High Genetic Diversity ◽  
The Family ◽  
The Mean

ABSTRACT The Neotropical freshwater catfish Pseudopimelodus atricaudus and Pseudopimelodus magnus are two recently discovered species endemic to the Colombian Magdalena-Cauca River basin. In this study, a set of 13 microsatellite loci were developed by using next generation sequence technology to assess the genetic diversity and population structure in P. atricaudus and test for cross-species amplification in P. magnus. Both species exhibited high genetic diversity (P. atricaudus: Na: 9.000 - 9.769 alleles/locus, Ho: 0.760 - 0.804, HE: 0.804 - 0.840; P. magnus: Na: 12.8 - 5.4 alleles/locus, Ho: 0.638 - 0.683, HE: 0.747 - 0.755) compared to the mean levels of genetic diversity reported for Neotropical Siluriformes, and lack of genetic differentiation among sampling sites within the Cauca River (P. atricaudus: F’ST=0.013 - 0.017, P > 0.05, D’est= -0.004 - 0.023, P > 0.05; P. magnus: F’ST= 0.031, P= 0.055; D’est= 0.045, P= 0.058). This work is the first insight on the diversity and the population genetics of species of the family Pseudopimelodidae and provides a framework to further population genetic and conservation analyses needed in this poorly studied family at the microevolutionary level.

scholarly journals Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication

2021 ◽  
Vol 134 (5) ◽  
pp. 1343-1362
Author(s):  
Alex C. Ogbonna ◽  
Luciano Rogerio Braatz de Andrade ◽  
Lukas A. Mueller ◽  
Eder Jorge de Oliveira ◽  
Guillaume J. Bauchet
Keyword(s):  
Population Genetics ◽  
Population Structure ◽  
Manihot Esculenta ◽  
Ex Situ ◽  
Germplasm Bank ◽  
Effective Population ◽  
Manihot Esculenta Crantz ◽  
Genetic Groups ◽  
Population Structure Analysis ◽  
Modern Breeding

Abstract Key message Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Abstract Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300–4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity $$({H}_{o})$$ ( H o ) , effective population size estimate $$\widehat{{(N}_{e}}$$ ( N e ^ ) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava’s center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

scholarly journals Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Fehintola V. Ajogbasile ◽  
Adeyemi T. Kayode ◽  
Paul E. Oluniyi ◽  
Kazeem O. Akano ◽  
Jessica N. Uwanibe ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Control Strategies ◽  
Population Diversity ◽  
Parasite Population ◽  
Nested Polymerase Chain Reaction ◽  
Public Health Burden ◽  
Genetic Diversity And Structure

Abstract Background Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. Methods In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. Results Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008–0.105, AMOVA: 0.039). Conclusion The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.

scholarly journals Genetic diversity, population structure, and effective population size in two yellow bat species in south Texas

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10348
Author(s):  
Austin S. Chipps ◽  
Amanda M. Hale ◽  
Sara P. Weaver ◽  
Dean A. Williams
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
North America ◽  
Wind Energy ◽  
Population Size ◽  
Effective Population Size ◽  
Microsatellite Loci ◽  
South Texas ◽  
Population Substructure ◽  
Effective Population

There are increasing concerns regarding bat mortality at wind energy facilities, especially as installed capacity continues to grow. In North America, wind energy development has recently expanded into the Lower Rio Grande Valley in south Texas where bat species had not previously been exposed to wind turbines. Our study sought to characterize genetic diversity, population structure, and effective population size in Dasypterus ega and D. intermedius, two tree-roosting yellow bats native to this region and for which little is known about their population biology and seasonal movements. There was no evidence of population substructure in either species. Genetic diversity at mitochondrial and microsatellite loci was lower in these yellow bat taxa than in previously studied migratory tree bat species in North America, which may be due to the non-migratory nature of these species at our study site, the fact that our study site is located at a geographic range end for both taxa, and possibly weak ascertainment bias at microsatellite loci. Historical effective population size (NEF) was large for both species, while current estimates of Ne had upper 95% confidence limits that encompassed infinity. We found evidence of strong mitochondrial differentiation between the two putative subspecies of D. intermedius (D. i. floridanus and D. i. intermedius) which are sympatric in this region of Texas, yet little differentiation using microsatellite loci. We suggest this pattern is due to secondary contact and hybridization and possibly incomplete lineage sorting at microsatellite loci. We also found evidence of some hybridization between D. ega and D. intermedius in this region of Texas. We recommend that our data serve as a starting point for the long-term genetic monitoring of these species in order to better understand the impacts of wind-related mortality on these populations over time.

Eight Novel Microsatellite Loci Developed from Vernal Pool Fairy Shrimp

2013 ◽  
Vol 4 (1) ◽  
pp. 134-138 ◽  
Author(s):  
Kristy Deiner ◽  
Joshua M. Hull ◽  
Bernie May
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Microsatellite Loci ◽  
Vernal Pool ◽  
Fairy Shrimp ◽  
Genomic Libraries ◽  
Primer Sets ◽  
Branchinecta Lynchi

Abstract We developed primer sets for eight di-, tri-, and tetranucleotide microsatellite loci for the threatened vernal pool fairy shrimp Branchinecta lynchi from CA, CAA, ATG, CAGA, and TAGA enriched genomic libraries. We tested primers in 74 individuals of B. lynchi from California, as well as 19 individuals from six other Branchinecta species: B. coloradensis, B. constricta, B. dissimilis, B. lindahli, B. mesovalensis, and B. oriena. The eight loci showed sufficient variability for investigations of B. lynchi evolution, population structure, and genetic diversity and may provide a new tool for assisting in delineation of management areas.

Sign in / Sign up

Export Citation Format

Share Document