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

2020 ◽  
Author(s):  
Pamela Vega-Polo ◽  
Maria M. 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 ◽  
Distance Model

AbstractThe 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 homologous SSR 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 to 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 the development of conservation programs for this valuable biological and cultural resource and for the páramo ecosystems as a whole.

Genetic diversity and conservation of the endemic tuco-tuco Ctenomys ibicuiensis (Rodentia: Ctenomyidae)

2020 ◽  
Author(s):  
Mayara Delagnelo Medeiros ◽  
Daniel Galiano ◽  
Bruno Busnello Kubiak ◽  
Paula Angélica Roratto ◽  
Thales Renato Ochotorena de Freitas
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Environmental Changes ◽  
Isolation By Distance ◽  
Conservation Status ◽  
Significant Risk ◽  
Structured Populations ◽  
Small Range ◽  
High Genetic Diversity ◽  
Landscape Modification

Abstract Endemic, small range species are susceptible to environmental changes and landscape modification. Understanding genetic diversity and distributional patterns is important for implementation of effective conservation measures. In this context, genetic diversity was evaluated to update the conservation status of an endemic tuco-tuco, Ctenomys ibicuiensis. Phylogeographic and population genetic analyses of mitochondrial DNA and microsatellite loci were carried out using 46 individuals sampled across the species’ distribution. Ctenomys ibicuiensis presented moderate to high genetic diversity and highly structured populations with low levels of gene flow and isolation by distance. Anthropogenic landscape changes threaten this restricted-range tuco-tuco. Considering its limited geographic distribution and highly structured populations with low gene flow, we consider C. ibicuiensis to be at significant risk of extinction.

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 Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1309
Author(s):  
Veronika Kharzinova ◽  
Arsen Dotsev ◽  
Anastasiya Solovieva ◽  
Olga Sergeeva ◽  
Georgiy Bryzgalov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Rangifer Tarandus ◽  
Allelic Richness ◽  
Environmental Changes ◽  
Principal Component ◽  
Genetic Structuring ◽  
Habitat Location ◽  
The Republic ◽  
Insight Into

To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka–Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes.

scholarly journals High genetic diversity but no geographical structure of Aedes albopictus populations in Réunion Island

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Anne C. Latreille ◽  
Pascal Milesi ◽  
Hélène Magalon ◽  
Patrick Mavingui ◽  
Célestine M. Atyame
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Aedes Albopictus ◽  
Genetic Variance ◽  
Mosquito Control ◽  
Isolation By Distance ◽  
Virus Transmission ◽  
Reunion Island ◽  
High Genetic Diversity ◽  
Réunion Island

Abstract Background In recent years, the Asian tiger mosquito Aedes albopictus has emerged as a species of major medical concern following its global expansion and involvement in many arbovirus outbreaks. On Réunion Island, Ae. albopictus was responsible for a large chikungunya outbreak in 2005–2006 and more recently an epidemic of dengue which began at the end of 2017 and is still ongoing at the time of writing. This dengue epidemic has seen a high number of human cases in south and west coastal regions, while few cases have been reported in the north and east of the island. To better understand the role of mosquito populations in such spatial patterns of dengue virus transmission in Réunion Island, we examined the genetic diversity and population structure of Ae. albopictus sampled across the island. Results Between November 2016 and March 2017, a total of 564 mosquitoes were collected from 19 locations in three main climatic regions (West, East and Center) of Réunion Island and were genotyped using 16 microsatellite loci. A high genetic diversity was observed with 2–15 alleles per locus and the average number of alleles per population varying between 4.70–5.90. Almost all FIS values were significantly positive and correlated to individual relatedness within populations using a hierarchical clustering approach based on principal components analyses (HCPC). However, the largest part of genetic variance was among individuals within populations (97%) while only 3% of genetic variance was observed among populations within regions. Therefore, no distinguishable population structure or isolation by distance was evidenced, suggesting high rates of gene flow at the island scale. Conclusions Our results show high genetic diversity but no genetic structure of Ae. albopictus populations in Réunion Island thus reflecting frequent movements of mosquitoes between populations probably due to human activity. These data should help in the understanding of Ae. albopictus vector capacity and the design of effective mosquito control strategies.

scholarly journals Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1441
Author(s):  
Filippo Cendron ◽  
Francesco Perini ◽  
Salvatore Mastrangelo ◽  
Marco Tolone ◽  
Andrea Criscione ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Conservation Status ◽  
Geographical Area ◽  
Snp Array ◽  
Local Economy ◽  
Conservation Strategies ◽  
Snp Analysis ◽  
Runs Of Homozygosity ◽  
Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

Genetic diversity of the lichen-forming alga, Diplosphaera chodatii, in North America and Europe

2013 ◽  
Vol 45 (6) ◽  
pp. 799-813 ◽  
Author(s):  
Kyle M. FONTAINE ◽  
Elfie STOCKER-WÖRGÖTTER ◽  
Tom BOOTH ◽  
Michele D. PIERCEY-NORMORE
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
North America ◽  
Isolation By Distance ◽  
Water Level Fluctuations ◽  
Free Living ◽  
Climatic Zones ◽  
Algal Symbiont ◽  
Low Levels

AbstractDermatocarpon luridum is a subaquatic lichen which is distributed within temperate climatic zones around the world. It colonizes rock substrata along the shoreline of lakes and rivers of watersheds that regularly experience water level fluctuations. The mycobiont produces perithecia with small, simple spores that are thought to be wind dispersed. The photobiont, Diplosphaera chodatii, occurs both free-living and lichenized but little is known about its distribution and dispersal. The goal of this study was to compare the population structure of the photobiont from lakes and rivers in central North America with those of Europe. Specimens were collected in Manitoba, Canada and Austria. Population structure of the algal symbiont was assessed using the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) and actin gene sequences. Results showed that genetic diversity and gene flow was high within local populations, but gene flow was low between continental populations. Low levels of gene flow between the most distant populations support the isolation-by-distance theory. The photobiont on both continents is also reported to be the photobiont for other lichen species contributing to photobiont availability for D. luridum.

scholarly journals Detection of Genetic Variation and Genetic Diversity in Two Indian Mudskipper Species (Boleophthalmus boddarti, B. dussumieri) using RAPD Marker

2013 ◽  
Vol 5 (2) ◽  
pp. 139-143
Author(s):  
Vellaichamy RAMANADEVI ◽  
Muthusamy THANGARAJ ◽  
Anbazhagan SURESHKUMAR ◽  
Jayachandran SUBBURAJ
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Environmental Changes ◽  
Genetic Relationships ◽  
Rapd Marker ◽  
Distinct Species ◽  
Fish Population ◽  
Habitat Destruction ◽  
Arbitrary Primers ◽  
Vellar Estuary

Due to the environmental changes and habitat destruction the mudskipper fish population is decreasing in recent years. To predict the fish population structure, frequent manual survey and molecular methods are widely used. Molecular markers such as RAPD, microsatellite, allozyme, D-loop haplotype are frequently adopted to assess the population structure of an organism. In this study ten- arbitrary primers were screened to estimate the genetic relationships and diversity of two mudskipper species (Boleophthalmus boddarti and B. dussumieri) in Vellar estuary, Tamilnadu, India. By this RAPD marker study, the genetic diversity (H) in B. boddarti was more (0.0116 ± 0.0066) than in B. dussumieri (0.0056 ± 0.0024) in Vellar estuary (India). The genetic distance between B. boddarti and B. dussumieri was 1.7943. By observing the species specific bands and the phylogenetic analysis it is revealed that these two species clearly deviated into separate clusters emphasizing the distinct species status.

scholarly journals Genetic Diversity and Population Structure of Wild Sunflower (Helianthus annuus L.) in Argentina: Reconstructing Its Invasion History

2019 ◽  
Vol 110 (6) ◽  
pp. 746-759 ◽  
Author(s):  
Fernando Hernández ◽  
Alejandro Presotto ◽  
Mónica Poverene ◽  
Jennifer R Mandel
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Chloroplast Genome ◽  
Helianthus Annuus ◽  
Ecological Factors ◽  
Invasion History ◽  
Phenotypic Data ◽  
Wild Sunflower ◽  
Multiple Introductions ◽  
Helianthus Annuus L

Abstract Studying the levels and patterns of genetic diversity of invasive populations is important to understand the evolutionary and ecological factors promoting invasions and for better designing preventive and control strategies. Wild sunflower (Helianthus annuus L.) is native to North America and was introduced, and has become invasive, in several countries, including Argentina (ARG). Here, using classical population genetic analyses and approximate Bayesian computation (ABC) modeling, we studied the invasion history of wild sunflower in ARG. We analyzed 115 individuals belonging to 15 populations from ARG (invasive range) and United States (US, native range) at 14 nuclear and 3 chloroplast simple sequence repeat markers along with 23 phenotypic variables. Populations from ARG showed similar levels of nuclear genetic diversity to US populations and higher genetic diversity in the chloroplast genome, indicating no severe genetic bottlenecks during the invasion process. Bayesian clustering analysis, based on nuclear markers, suggests the presence of 3 genetic clusters, all present in both US and ARG. Discriminant analysis of principal components (DAPC) detected an overall low population structure between central US and ARG populations but separated 2 invasive populations from the rest. ABC modeling supports multiple introductions but also a southward dispersal within ARG. Genetic and phenotypic data support the central US as a source of introduction while the source of secondary introductions could not be resolved. Finally, using genetic markers from the chloroplast genome, we found lower population structure in ARG when compared with US populations, suggesting a role for seed-mediated gene flow in Argentina.

Molecular systematics reveals multiple lineages and cryptic speciation in the freshwater crayfish Parastacus brasiliensis (von Martens, 1869) (Crustacea : Decapoda : Parastacidae)

2018 ◽  
Vol 32 (6) ◽  
pp. 1265 ◽  
Author(s):  
Ivana Miranda ◽  
Kelly M. Gomes ◽  
Felipe B. Ribeiro ◽  
Paula B. Araujo ◽  
Catherine Souty-Grosset ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Isolation By Distance ◽  
Conservation Status ◽  
Sensu Stricto ◽  
Genetic Distances ◽  
Distribution Data ◽  
Lake Basin ◽  
Gene Pools ◽  
Freshwater Crayfish ◽  
Isolated Populations

The characterisation of intraspecific genetic diversity in representatives of the South American crayfish genus Parastacus Huxley, 1879 is here carried out for the first time by comparing populations of Parastacus brasiliensis (von Martens, 1869) as currently defined. Phylogenetic reconstructions based on mitochondrial and nuclear markers indicate the existence of multiple lineages, of which only one can be considered as P. brasiliensis sensu stricto. In addition, there are seven other lineages, one of which is the subspecies Parastacus brasiliensis promatensis Fontoura &amp; Conter, 2008, which is here elevated to species level. We thereby increase to 14 the number of recognised species within Parastacus in South America. Genetic distances among P. brasiliensis sensu stricto and the lineages ‘A’, ‘B’ and ‘C’ increase with geographical distances, suggesting isolation by distance as an important driver of diversification, and eventually speciation, in these burrowing crayfishes. Parastacus brasiliensis occurs mainly in the Guaíba Lake basin and studied populations show limited connectivity and gene flow, probably due to habitat fragmentation. On the basis of genetic and distribution data, the conservation status of P. brasiliensis sensu stricto is confirmed as Near Threatened (NT). These findings lead us to encourage the establishment of preservation areas for isolated populations. The importance of preserving the newly recognised distinct gene pools in order to maintain overall genetic diversity is emphasised.

Sign in / Sign up

Export Citation Format

Share Document