Historical migration and taxonomic entity of Korean endemic shrub Lespedeza maritima (Fabaceae) based on microsatellite loci

Abstract Various plant species are endemic to the Korean Peninsula, but their evolutionary divergence and establishment are poorly understood. One of these, Lespedeza maritima, has been proposed as either a hybrid (L. cyrtobotrya × L. maximowiczii) or a synonym of L. thunbergii. A distinct taxon, L. uekii, has been proposed for inland populations. We investigated genetic diversity and structure in L. maritima and related taxa to resolve this. Genotypes of L. maritima (n = 244, including L. uekii) were determined using 12 microsatellite loci, then compared with those of related species. Genetic diversity within L. maritima was estimated, and Bayesian clustering analysis was used to represent its genetic structure and that of related taxa. Its distribution during the last glacial maximum (LGM) was predicted using ecological niche modelling (ENM). Neighbour-joining (NJ) analysis and principal coordinate analysis (PCoA) were used to investigate relationships among species. Bayesian tree based on nuclear ribosomal internal transcribed spacers (nrITS) was also reconstructed to show relationships and divergence time among species. Morphological features were examined using flower characteristics. In result, expected heterozygosity (HE) and allelic richness (AR) within L. maritima were higher in southern than northern populations. Bayesian clustering analysis largely assigned populations to two clusters (K = 2) (south vs. north). The ENM showed that L. maritima occurred around the East China Sea and Korean Strait land bridge during the LGM. Compared with other Lespedeza species, L. maritima was assigned to an independent cluster (K = 2–5), supported by the NJ, PCoA, Bayesian tree and morphological examination results. Lespedeza maritima and L. uekii were clustered to one clade on Bayesian tree. Given results, current L. maritima populations derive from post-LGM colonization away from southern refugia. The type L. uekii, which grows inland, is thought synonym of L. maritima. In addition, L. maritima is considered a distinct species, compared with related taxa.

Download Full-text

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

Malaria Journal ◽

10.1186/s12936-021-03734-x ◽

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.

Download Full-text

New microsatellite loci for estimating genetic diversity and structure in Octopus hubbsorum from Nayarit, México

Molecular Biology Reports ◽

10.1007/s11033-021-06601-9 ◽

2021 ◽

Vol 48 (10) ◽

pp. 7007-7012

Author(s):

José de Jesús Dueñas-Romero ◽

José Francisco Domínguez-Contreras ◽

Jasmín Granados-Amores ◽

Adrián Munguía-Vega ◽

Francisco Javier García-Rodríguez

Keyword(s):

Genetic Diversity ◽

Microsatellite Loci ◽

Genetic Diversity And Structure

Download Full-text

Consequences of long- and short-term fragmentation on the genetic diversity and differentiation of a late successional rainforest conifer

Australian Journal of Botany ◽

10.1071/bt10291 ◽

2011 ◽

Vol 59 (4) ◽

pp. 351 ◽

Cited By ~ 15

Author(s):

Rohan Mellick ◽

Andrew Lowe ◽

Maurizio Rossetto

Keyword(s):

Genetic Diversity ◽

New South ◽

Demographic Stochasticity ◽

Niche Modelling ◽

Lag Effects ◽

South Wales ◽

Unique System ◽

Genetic Diversity And Structure ◽

Modelling Techniques ◽

Diversity Estimates

The east Australian rainforests provide a unique system with which to study historic climate-driven habitat fragmentation. The long life span of rainforest conifers and consequent lag effects on genetic variation, offer insights into demographic stochasticity in small populations and persistence in increasingly fragmented systems. Microsatellite markers were used to investigate the genetic diversity and structure of Podocarpus elatus (Podocarpaceae), a long-lived rainforest conifer endemic to Australia. Twenty-seven populations throughout the east Australian rainforests were screened and two divergent regions separated by the dry Clarence River valley (New South Wales) were discovered. This biogeographic barrier may be referred to as the Clarence River Corridor. Niche modelling techniques were employed to verify the incidence of habitat divergence between the two regions. Significantly high inbreeding was detected throughout the species range with no evidence of recent bottlenecks. Most of the diversity in the species resides between individuals within populations, which suggest the species would be sensitive to the adverse effects of inbreeding, yet evidence suggests that these populations have been small for several generations. Slightly higher diversity estimates were found in the southern region, but it is likely that the species survived historic population contraction in dispersed refugia within each of these genetically differentiated regions.

Download Full-text

Population genetics of the freshwater fish Prochilodus magdalenae (Characiformes: Prochilodontidae), using species-specific microsatellite loci

PeerJ ◽

10.7717/peerj.10327 ◽

2020 ◽

Vol 8 ◽

pp. e10327

Author(s):

Ricardo M. Landínez-García ◽

Juan Carlos Narváez ◽

Edna J. Márquez

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Freshwater Fish ◽

Microsatellite Loci ◽

Natural Populations ◽

Genetic Stock ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Genetic Stocks ◽

Species Specific

Prochilodus magdalenae is a freshwater fish endemic to the Colombian Magdalena-Cauca and Caribbean hydrographic basins. The genetic structure patterns of populations of different members of Prochilodus and the historic restocking of its depleted natural populations suggest that P. magdalenae exhibits genetic stocks that coexist and co-migrate throughout the rivers Magdalena, Cauca, Cesar, Sinú and Atrato. To test this hypothesis and explore the levels of genetic diversity and population demography of 725 samples of P. magdalenae from the studied rivers, we developed a set of 11 species-specific microsatellite loci using next-generation sequencing, bioinformatics, and experimental tests of the levels of diversity of the microsatellite loci. The results evidenced that P. magdalenae exhibits high genetic diversity, significant inbreeding coefficient ranging from 0.162 to 0.202, and signs of erosion of the genetic pool. Additionally, the population genetic structure constitutes a mixture of genetic stocks heterogeneously distributed along the studied rivers, and moreover, a highly divergent genetic stock was detected in Chucurí, Puerto Berrío and Palagua that may result from restocking practices. This study provides molecular tools and a wide framework regarding the genetic diversity and structure of P. magdalenae, which is crucial to complement its baseline information, diagnosis and monitoring of populations, and to support the implementation of adequate regulation, management, and conservation policies.

Download Full-text

The impact of Pleistocene sea-level oscillations on plant genetic diversity: the case of the western Mediterranean endemic Carduncellus dianius (Asteraceae)

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boz058 ◽

2019 ◽

Vol 191 (3) ◽

pp. 399-420

Author(s):

Sonia Herrando-Moraira ◽

Sergi Massó ◽

Deborah Zani ◽

Jordi López-Pujol ◽

Roser Vilatersana

Keyword(s):

Genetic Diversity ◽

Sea Level ◽

Plastid Dna ◽

Western Mediterranean ◽

Early Pleistocene ◽

Niche Modelling ◽

Long Distance ◽

Sea Level Fluctuations ◽

Genetic Diversity And Structure ◽

The Impact

Abstract To what extent Pleistocene sea-level fluctuations have affected the genetic diversity of species is one of the current topics in biogeographical research. Carduncellus dianius is a Mediterranean narrow endemic species, restricted to < 20 populations distributed along coastal areas in Alicante (mainland eastern Iberian Peninsula) and on the island of Ibiza (Balearic Islands). To get insights into its evolutionary history and its genetic diversity and structure, we combined the analysis of molecular markers (three plastid DNA regions and AFLP) with ecological niche modelling. Results from dated phylogeographical analyses revealed that this species might have originated in the continental region during the early Pleistocene. The colonization of Ibiza could have occurred by a single long-distance dispersal event, with a subsequent back-colonization from the island to the same continental area of origin. These results corroborate the role of islands as sources for mainland colonization (biodiversity reservoirs) and as refugia during glacial periods. Notably, we detected that populations located on stable landmasses (i.e. not affected by sea rising during interglacial cycles) harboured significantly higher genetic diversity than those that were periodically submerged during the periods of marine transgressions. Our results point out sea-level fluctuations as a factor to be considered in phylogeographical studies focused on species distributed along coastlines.

Download Full-text

Response of xerophytic plants to glacial cycles in southern South America

Annals of Botany ◽

10.1093/aob/mcy235 ◽

2019 ◽

Vol 124 (1) ◽

pp. 15-26 ◽

Cited By ~ 1

Author(s):

Carmen G Ossa ◽

Paz Montenegro ◽

Isabel Larridon ◽

Fernanda Pérez

Keyword(s):

Genetic Diversity ◽

Isolation By Distance ◽

Population History ◽

Arid Environments ◽

Glacial Cycles ◽

Niche Modelling ◽

Climatic Niche ◽

Range Contraction ◽

Genetic Diversity And Structure ◽

Semi Arid

Abstract Background and Aim Quaternary glaciations strongly affected the distribution of species from arid and semi-arid environments, as temperature drops were accompanied by strong fluctuations in rainfall. In this study, we examined the response of xerophytic species to glacial cycles, determining the genetic patterns and climatic niche of Echinopsis chiloensis var. chiloensis, an endemic columnar cactus of arid and semi-arid regions of Chile. Methods We analysed 11 polymorphic microsatellites for 130 individuals from 13 populations distributed across the entire distribution of the species. We examined genetic diversity and structure, identified possible patterns of isolation by distance (IBD) and tested two competing population history scenarios using Approximate Bayesian Computation. The first scenario assumes a constant population size while the second includes a bottleneck in the southern population. The latter scenario assumed that the southernmost populations experienced a strong contraction during glaciation, followed by a postglacial expansion; by contrast, the area of the northernmost populations remained as a stable refugium. We also used ecological niche modelling (ENM) to evaluate the location and extension of suitable areas during the Last Glacial Maximum (LGM) and the mid-Holocene. Key Results We found a decline in genetic diversity towards high latitudes and a significant IBD pattern that together with ENM predictions suggest that E. chiloensis var. chiloensis experienced range contraction northwards during wet–cold conditions of the LGM, followed by expansion during aridification of the mid-Holocene. In addition to IBD, we detected the presence of a strong barrier to gene flow at 32°30′S, which according to coalescence analysis occurred 44 kyr BP. The resulting genetic clusters differed in realized climatic niche, particularly in the variables related to precipitation. Conclusions Our results suggest that the cactus E. chiloensis var. chiloensis experienced range contraction and fragmentation during the wet–cold conditions of the LGM, which may have facilitated ecological differentiation between northern and southern populations, promoting incipient speciation.

Download Full-text

Genetic diversity and structure of Astrocaryum jauari (Mart.) palm in two Amazon river basins

Cropp Breeding and Applied Biotechnology ◽

10.1590/1984-70332014v14n3a25 ◽

2014 ◽

Vol 14 (3) ◽

pp. 166-173 ◽

Cited By ~ 4

Author(s):

Liliane D. Santos Oliveira ◽

Santiago L. Ferreyra Ramos ◽

Maria T. Gomes Lopes ◽

Gabriel Dequigiovanni ◽

Elizabeth Ann Veasey ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Genetic Structure ◽

Microsatellite Loci ◽

Plant Material ◽

Spatial Genetic Structure ◽

River Basins ◽

Genetic Analyses ◽

Main River ◽

Genetic Diversity And Structure

Astrocaryum jauari is a non-domesticated palm that is exploited by poachers. Our objective was to investigate the organization of the geneticdiversity and structure of three A. jauari populations. The study was carried out in the state of Amazonas, between the municipalities of Coari and Manaus. Nine microsatellite loci were used for the genetic analyses. High genetic variation was found, with a mean number of alleles per locus varying from 3.9 to 4.4. The average observed heterozygosity, varying from 0.71 to 0.78, was higher than expected. No spatial genetic structure was detected, since only one cluster was observed. Our results indicate a possible dispersion strategy and suggest that conservation measures of this species should focus mainly on the populations found at the end of the main river (Solimões) where most of the plant material originating from the headwaters of the tributaries of this river is concentrated.

Download Full-text

GENETIC DIVERSITY AND STRUCTURE OF Oenocarpus mapora GERMPLASM CONSERVED AT EASTERN AMAZON

Revista Brasileira de Fruticultura ◽

10.1590/0100-2945-208/14 ◽

2015 ◽

Vol 37 (4) ◽

pp. 984-992

Author(s):

ELISA FERREIRA MOURA ◽

MARIA DO SOCORRO PADILHA DE OLIVEIRA ◽

DIEHGO TULOZA DA SILVA ◽

LÍGIA CRISTINE GONÇALVES PONTES

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Microsatellite Loci ◽

Natural Populations ◽

Brazilian Amazon ◽

Germplasm Bank ◽

Analysis Of Molecular Variance ◽

Molecular Variance ◽

Total Genetic Diversity ◽

Genetic Diversity And Structure

ABSTRACT The aim of this study was to evaluate the genetic diversity and structure in the germoplasm of Oenocarpus mapora conserved at Eastern Amazon. Thus, 88 individuals were genotyped with five microsatellite loci. These individuals belong to 24 accessions that were sampled in eight sample places of three Brazilian Amazon states conserved at the Active Germplasm Bank (AGB) of Embrapa Eastern Amazon. All loci were polymorphic and they generated 85 alleles with an average of 17 alleles per loci. Total genetic diversity (HE) was 0.48. Sample places were considered genetically distinct, with ?p = 0.354. The analysis of molecular variance (AMOVA) identified that the genetic portion among areas was of 36.14% and within 63.86%. The Nei distances varied from 0.091 between Abaetetuba and Santo Antônio do Tauá, both in the state of Pará (PA), to 4.18, between Parintins, AM and Rio Branco, AC. By means of Bayesian analysis, it was identified nine clusters that compose the accessions of the germplasm bank, with different distributions among individuals. The study showed high fixation rates per sample area, which indicates that there may have been significant inbreeding or crossing among parental individuals. It suggests that future samples should be made of different plants in natural populations. Even though, it was verified that there is considerable genetic variation in the germplasm of O. mapora.

Download Full-text

Morphological and genetic diversity of traditional varieties of agave in Hidalgo State, Mexico

PLoS ONE ◽

10.1371/journal.pone.0254376 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0254376

Author(s):

Carmen Julia Figueredo-Urbina ◽

Gonzalo D. Álvarez-Ríos ◽

Mario Adolfo García-Montes ◽

Pablo Octavio-Aguilar

Keyword(s):

Genetic Diversity ◽

Bayesian Clustering ◽

Structured Interviews ◽

Domestication Syndrome ◽

Cultural Importance ◽

Genetic Groups ◽

Expected Heterozygosity ◽

Genetic Diversity And Structure ◽

Agave Americana ◽

Distilled Beverages

The agaves are plants of cultural importance which have been used by humans for about 10,000 years and about 40 specific uses. The most culturally and economically important of those uses are for the production of fermented (pulque) and distilled beverages (mescal). Pulque continues to be produced in nearly all of Mexico, and the agaves used for this purpose have shown domestication syndrome. We carry out an ethnobotanical, morphological, and genetic analysis of the traditional varieties of pulque agave used in the production of aguamiel (agave sap) and pulque in the state of Hidalgo. We did semi-structured interviews, free listings, and tours with 11 agave managers. We analyzed morphology and studied genetic diversity and structure using nuclear microsatellites. We found wild-collected, tolerated, transplanted, and cultivated varieties of agave. This comprised 19 traditional varieties of pulque agave, 12 of them in production during the study, which corresponded to the species Agave americana, A. salmiana y A. mapisaga and five intraspecific entities. The varieties were grouped morphologically according to a management gradient; the wild-collected varieties were the smallest, with more lateral teeth and a larger terminal spine. The cultivated varieties clearly exhibited domestication syndrome, with larger plants and smaller dentition. The expected heterozygosity (He) of the varieties ranged from 0.204 to 0.721. Bayesian clustering suggested the existence of three genetic groups, both at the level of traditional varieties of pulque agaves and for management categories, a result that matches multivariate clustering. Pulque producers in the studied localities maintain high agrobiodiversity. The cultivated varieties exhibit domestication syndrome, as has been reported for other species of the genus with the same selection purposes. Our results support the hypothesis of a decrease in genetic diversity in crops compared to wild-growing agaves, which seems to be due to vegetative propagation, among other factors.

Download Full-text

Genetic Diversity and Structure of the Nile Soft-Shelled Turtle (Trionyx triunguis) Along the Mediterranean coast of Turkey

Russian Journal of Herpetology ◽

10.30906/1026-2296-2020-27-6-307-315 ◽

2020 ◽

Vol 27 (6) ◽

pp. 307-315

Author(s):

Özgür Güçlü ◽

Bülent Bozdoğan

Keyword(s):

Microsatellite Loci ◽

Geographic Distance ◽

Iucn Red List ◽

Genetic Variations ◽

Mediterranean Coast ◽

Critically Endangered ◽

Mediterranean Populations ◽

Genetic Diversity And Structure ◽

Polymorphic Microsatellite ◽

The Mediterranean

The Nile soft-shelled turtle (Trionyx triunguis) is distributed between Dalyan and Samandağ throughout the Mediterranean coast in Turkey. The Mediterranean subpopulation of the Nile soft-shelled turtle is listed as critically endangered in the IUCN Red List Categories. This investigation aimed to determinate levels of genetic variations and patterns of genetic structures among Mediterranean populations in Turkey by using T. triunguis-specific microsatellite primers. A total of 13 polymorphic microsatellite loci were studied among samples of 121 individuals collected from five populations in Turkey. Of 13 polymorphic microsatellite loci used, 3 new were identified in this study. The genetic differentiation among the 5 studied populations of T. triunguis was significant (p 0.001). The analysis of molecular variance (AMOVA) indicated that genetic variations occurred mainly within populations (89.7%) rather than among populations (10.3%). Structure analysis showed presence of two main groups among the Mediterranean T. triunguis populations. However genetic variations among populations were not correlated with geographic distance between the locations. Analysis of data showed that one of the populations (Dalyan) had undergone a bottleneck effect. Migration analysis indicates that T. triunguis migrates between five Mediterranean populations in Turkey. We concluded that based on our results the status of ‘critically endangered’ of T. triunguis should be maintained. Long term population genetic survey studies should be undertaken and changes in habitats of T. triunguis populations, as well as their population size and structure should be monitored for each population to be able to establish a clear strategy for protection of T. triunguis.

Download Full-text