scholarly journals Contrasting effects of local environment and grazing pressure on the genetic diversity and structure of Artemisia frigida

2021 ◽  
Author(s):  
Khurelpurev Oyundelger ◽  
Veit Herklotz ◽  
Dörte Harpke ◽  
Batlai Oyuntsetseg ◽  
Karsten Wesche ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Isolation By Distance ◽  
Grazing Intensity ◽  
Population Level ◽  
Local Environment ◽  
Grazing Pressure ◽  
Climatic Gradient ◽  
Genetic Structuring ◽  
Artemisia Frigida ◽  
Genetic Diversity And Structure

AbstractDrylands count among the most globally extensive biomes, and while many desert and dry rangeland ecosystems are under threat, genetic structures of dryland species are still rarely studied. Artemisia frigida is one of the most widely distributed plant species in the temperate rangelands of Eurasia and North America, and it also dominates in many habitats of Mongolia due to its tolerance to low temperatures, drought and disturbance. Local environmental conditions and grazing pressure can influence species performance and affect spatial patterns of genetic diversity in contrasting ways, and our study set out to evaluate such effects on the genetic diversity and structure of A. frigida. We first developed new species-specific Simple Sequence Repeats (SSRs) markers using whole genome sequencing. We then analysed 11 populations of A. frigida that had been sampled along a large climatic gradient in Mongolia, which were sub-structured according to three levels of grazing intensity. Estimates of genetic diversity at the population level were high (HO = 0.56, HE = 0.73) and tended to increase with higher precipitation and soil nutrient availability. Grazing had no effect on genetic diversity, however, a high number of grazing-specific indicator alleles was found at grazed sites. Genetic differentiation among populations was extremely low (global GST = 0.034). Analysis of Molecular Variance revealed 5% variance between populations along the climatic gradient, with 3% of the variance being partitioned among different grazing intensity levels. We found no relationship between geographic and genetic distances, and thus no isolation by distance in this widely distributed species. The relatively low genetic structuring suggests that considerable gene flow exists among A. frigida populations across the rangelands of Mongolia, in spite of the pervasive grazing in the region.

scholarly journals Taxonomic Differentiation of Iberian Knapweeds (Centaurea sects. Jacea and Lepteranthus, Asteraceae) and Genetic Isolation of Infraspecific Floral Morphotypes

2020 ◽  
Vol 105 (4) ◽  
pp. 481-501
Author(s):  
Itziar Arnelas ◽  
Ernesto Pérez-Collazos ◽  
Juan A. Devesa ◽  
Antonio J. Manzaneda ◽  
Pilar Catalan
Keyword(s):  
Genetic Diversity ◽  
Isolation By Distance ◽  
Population Level ◽  
Potential Effect ◽  
Genetic Distances ◽  
Fixation Index ◽  
Genetic Isolation ◽  
Related Factors ◽  
Genetic Diversity And Structure ◽  
The Impact

The taxonomic boundaries of Centaurea L. species and infraspecific taxa are often blurred by hybridizations. However, counterbalancing genetic isolation contributes to maintaining taxonomic limits and fostering rapid speciation processes. Radiant (R) and non-radiant (NR) capitula are two major floral morphs present in Centaurea. However, it is unclear how gene flow affects the distribution of floral morphotypes across populations and taxa. We have investigated the taxonomic differentiation and potential effect of genetic isolation in R and NR populations of Iberian Centaurea sects. Jacea (Mill.) Pers. ex Dumort. and Lepteranthus (Neck. ex DC.) Dumort. A total of 510 individuals from 58 populations (12 taxa) were analyzed using 165 amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structure parameters were estimated at the taxon, population, and floral morphotypic levels. We tested whether there was correlation between population pairwise fixation index (Fst) genetic distances and the inbreeding coefficient (Fis), taken as a surrogate of reproductive isolation between the R and NR morphotypes of each group, and also taking into account geographic distances, using distance-based redundancy analysis (dbRDA). We also performed isolation by distance (IBD) tests between different floral morphotypes, aiming to infer the impact of genetic isolation on evolutionary and taxonomic divergence of the individuals. The taxa of Centaurea sects. Jacea and Lepteranthus constitute independent evolutionary lineages. Most of the detected genetic clusters match the taxonomic circumscription proposed in our most recent treatments. Genetic diversity was highest in C. debeauxii Godr. & Gren. subsp. debeauxii and subsp. grandiflora (Gaudin ex Schübl. & G. Martens) Devesa & Arnelas and in C. jacea L. subsp. angustifolia (DC.) Gremli (R) and lowest in C. nevadensis Boiss. & Reut. (NR) within the Centaurea sect. Jacea clade, whereas it was highest in C. linifolia L. within the Centaurea sect. Lepteranthus clade. Population-level dbRDA tests did not detect a significant correlation of R versus NR genetic distances and Fis values in any of the studied cases; by contrast, they detected significant correlation with longitude (C. jacea subsp. angustifolia, C. debeauxii, C. linifolia–C. stuessyi Arnelas, Devesa & E. López) or latitude (C. nigra L.). IBD analysis at the individual level showed that, in addition to geography, other morphotype-related factors may affect the genetic differentiation of R versus NR morphs in C. nigra, C. debeauxii, and C. linifolia–C. stuessyi. These results suggest that the fixation of the different morphs within the same taxon or group may be explained by geographic isolation, though we could not discount other potential unknown factors that could have contributed to microspeciation in these recently divergent populations, which originated only several thousands of years ago.

scholarly journals Pollen-mediated gene flow ensures connectivity among spatially discrete sub-populations of Phalaenopsis pulcherrima, a tropical food-deceptive orchid

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Zhe Zhang ◽  
Stephan W. Gale ◽  
Ji-Hong Li ◽  
Gunter A. Fischer ◽  
Ming-Xun Ren ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Polynomial Regression ◽  
Genetic Erosion ◽  
Population Level ◽  
Hainan Island ◽  
Paternity Analysis ◽  
Genetic Structuring ◽  
Long Distance ◽  
High Genetic Diversity

Abstract Background Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchid Phalaenopsis pulcherrima on Hainan Island, China. Results Phalaenopsis pulcherrima is self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules of P. pulcherrima to each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next. Conclusions Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity in P. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

Genetic diversity and structure of Jatropha curcas L. in its centre of origin

2014 ◽  
Vol 13 (1) ◽  
pp. 9-17 ◽  
Author(s):  
M. Salvador-Figueroa ◽  
J. Magaña-Ramos ◽  
J. A. Vázquez-Ovando ◽  
M. L. Adriano-Anaya ◽  
I. Ovando-Medina
Keyword(s):  
Genetic Diversity ◽  
Jatropha Curcas ◽  
Isolation By Distance ◽  
Random Mating ◽  
Mantel Test ◽  
Reproductive Pattern ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Centre Of Origin ◽  
Genetic Diversity And Structure

To investigate the genetic diversity and structure of Jatropha curcas L. oilseed plant, in this study, native populations from Chiapas, Mexico, were evaluated, using microsatellite DNA markers. A total of 93 representative samples were selected from seven sites in two regions in the state of Chiapas grouped by geographical proximity, where leaf samples were collected to isolate the genomic DNA. Individual polymerase chain reactions were carried out with ten pairs of specific oligonucleotides for the microsatellites of J. curcas, separating the products of amplification by acrylamide electrophoresis. Twenty-seven fragments were detected (77% polymorphic) with which heterozygous individuals were distinguished. The most informative microsatellite was Jcps20 (nine alleles, polymorphic index content 0.354). The average polymorphism per population was 58%. The Hardy–Weinberg tests revealed a reproductive pattern of non-random mating. The diversity descriptors and the analysis of molecular variance revealed that the populations were structured and moderately differentiated (FST 0.087) and that this differentiation was not due to isolation by distance, as the Mantel test was not significant (P= 0.137), but rather due to allopatry. Bayesian analysis revealed that the accessions belonged to only four genetic groups and confirmed the differentiation between the regions. Because some loci were in Hardy–Weinberg disequilibrium, it is proposed that differentiation is due to the clonal reproduction of J. curcas practised by farmers in Chiapas, along with the anthropogenic dispersion at regional levels. The results of this study reveal that J. curcas in Chiapas has genetic diversity that is greater than that reported in other parts of the world, which represents a potential germplasm pool for the selection of genotypes.

scholarly journals Does silvoagropecuary landscape fragmentation affect the genetic diversity of the sigmodontine rodent Oligoryzomys longicaudatus?

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3842 ◽  
Author(s):  
Daniela Lazo-Cancino ◽  
Selim S. Musleh ◽  
Cristian E. Hernandez ◽  
Eduardo Palma ◽  
Enrique Rodriguez-Serrano
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Landscape Fragmentation ◽  
Native Forest ◽  
Least Cost Path ◽  
Natural Habitats ◽  
Forest Patches ◽  
Genetic Diversity And Structure ◽  
Oligoryzomys Longicaudatus

Background Fragmentation of native forests is a highly visible result of human land-use throughout the world. In this study, we evaluated the effects of landscape fragmentation and matrix features on the genetic diversity and structure of Oligoryzomys longicaudatus, the natural reservoir of Hantavirus in southern South America. We focused our work in the Valdivian Rainforest where human activities have produced strong change of natural habitats, with an important number of human cases of Hantavirus. Methods We sampled specimens of O. longicaudatus from five native forest patches surrounded by silvoagropecuary matrix from Panguipulli, Los Rios Region, Chile. Using the hypervariable domain I (mtDNA), we characterized the genetic diversity and evaluated the effect of fragmentation and landscape matrix on the genetic structure of O. longicaudatus. For the latter, we used three approaches: (i) Isolation by Distance (IBD) as null model, (ii) Least-cost Path (LCP) where genetic distances between patch pairs increase with cost-weighted distances, and (iii) Isolation by Resistance (IBR) where the resistance distance is the average number of steps that is needed to commute between the patches during a random walk. Results We found low values of nucleotide diversity (π) for the five patches surveyed, ranging from 0.012 to 0.015, revealing that the 73 sampled specimens of this study belong to two populations but with low values of genetic distance (γST) ranging from 0.022 to 0.099. Likewise, we found that there are no significant associations between genetic distance and geographic distance for IBD and IBR. However, we found for the LCP approach, a significant positive relationship (r = 0.737, p = 0.05), with shortest least-cost paths traced through native forest and arborescent shrublands. Discussion In this work we found that, at this reduced geographical scale, Oligoryzomys longicaudatus shows genetic signs of fragmentation. In addition, we found that connectivity between full growth native forest remnants is mediated by the presence of dense shrublands and native forest corridors. In this sense, our results are important because they show how native forest patches and associated routes act as source of vector species in silvoagropecuary landscape, increasing the infection risk on human population. This study is the first approach to understand the epidemiological spatial context of silvoagropecuary risk of Hantavirus emergence. Further studies are needed to elucidate the effects of landscape fragmentation in order to generate new predictive models based on vector intrinsic attributes and landscape features.

scholarly journals Novel Microsatellite Markers Used for Determining Genetic Diversity and Tracing of Wild and Farmed Populations of the Amazonian Giant Fish Arapaima gigas

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1324
Author(s):  
Paola Fabiana Fazzi-Gomes ◽  
Jonas da Paz Aguiar ◽  
Diego Marques ◽  
Gleyce Fonseca Cabral ◽  
Fabiano Cordeiro Moreira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Amazon Basin ◽  
Population Level ◽  
Legal Aspects ◽  
Genetic Management ◽  
Genetic Structuring ◽  
Environmental Pressures ◽  
National Regulation ◽  
Arapaima Gigas

The Amazonian symbol fish Arapaima gigas is the only living representative of the Arapamidae family. Environmental pressures and illegal fishing threaten the species’ survival. To protect wild populations, a national regulation must be developed for the management of A. gigas throughout the Amazon basin. Moreover, the reproductive genetic management and recruitment of additional founders by aquaculture farms are needed to mitigate the damage caused by domestication. To contribute to the sustainable development, we investigated the genetic diversity of wild and cultivated populations of A. gigas and developed a panel composed by 12 microsatellite markers for individual and population genetic tracing. We analyzed 368 samples from three wild and four farmed populations. The results revealed low rates of genetic diversity in all populations, loss of genetic diversity and high inbreeding rates in farmed populations, and genetic structuring among wild and farmed populations. Genetic tracing using the 12 microsatellite markers was effective, and presented a better performance in identifying samples at the population level. The 12-microsatellite panel is appliable to the legal aspects of the trade of the A. gigas, such as origin discrimination, reproductive genetic management by DNA profiling, and evaluation and monitoring of genetic diversity.

scholarly journals Applied phylogeography of Cyclopia intermedia (Fabaceae) highlights the need for ‘duty of care’ when cultivating honeybush

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9818 ◽  
Author(s):  
Nicholas C. Galuszynski ◽  
Alastair J. Potts
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Cultivated Plants ◽  
Duty Of Care ◽  
Mountain Range ◽  
Wild Populations ◽  
Genetic Structuring ◽  
Mountain Ranges

Background The current cultivation and plant breeding of Honeybush tea (produced from members of CyclopiaVent.) do not consider the genetic diversity nor structuring of wild populations. Thus, wild populations may be at risk of genetic contamination if cultivated plants are grown in the same landscape. Here, we investigate the spatial distribution of genetic diversity within Cyclopia intermedia E. Mey.—this species is widespread and endemic in the Cape Floristic Region (CFR) and used in the production of Honeybush tea. Methods We applied High Resolution Melt analysis (HRM), with confirmation Sanger sequencing, to screen two non-coding chloroplast DNA regions (two fragments from the atpI-aptH intergenic spacer and one from the ndhA intron) in wild C. intermedia populations. A total of 156 individuals from 17 populations were analyzed for phylogeographic structuring. Statistical tests included analyses of molecular variance and isolation-by-distance, while relationships among haplotypes were ascertained using a statistical parsimony network. Results Populations were found to exhibit high levels of genetic structuring, with 62.8% of genetic variation partitioned within mountain ranges. An additional 9% of genetic variation was located amongst populations within mountains, suggesting limited seed exchange among neighboring populations. Despite this phylogeographic structuring, no isolation-by-distance was detected (p > 0.05) as nucleotide variation among haplotypes did not increase linearly with geographic distance; this is not surprising given that the configuration of mountain ranges dictates available habitats and, we assume, seed dispersal kernels. Conclusions Our findings support concerns that the unmonitored redistribution of Cyclopia genetic material may pose a threat to the genetic diversity of wild populations, and ultimately the genetic resources within the species. We argue that ‘duty of care’ principles be used when cultivating Honeybush and that seed should not be translocated outside of the mountain range of origin. Secondarily, given the genetic uniqueness of wild populations, cultivated populations should occur at distance from wild populations that is sufficient to prevent unintended gene flow; however, further research is needed to assess gene flow within mountain ranges.

Conservation implications of distinct genetic structuring in the endangered freshwater fish Nannoperca oxleyana (Percichthyidae)

2009 ◽  
Vol 60 (1) ◽  
pp. 34 ◽  
Author(s):  
James T. Knight ◽  
Catherine J. Nock ◽  
Martin S. Elphinstone ◽  
Peter R. Baverstock
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Sand Dunes ◽  
Restricted Gene Flow ◽  
Genetic Structuring ◽  
Conservation Implications ◽  
South Wales ◽  
Haplotypic Diversity ◽  
Genetic Diversity And Structure ◽  
Fragmented Distribution

The maintenance of genetic diversity and gene flow in threatened species is a vital consideration for recovery programs. The endangered Oxleyan pygmy perch Nannoperca oxleyana has a fragmented distribution within coastal freshwater drainages of southern Queensland and northern New South Wales, Australia. In the present study, mitochondrial DNA control region variation was used to assess genetic diversity and structure across the geographical range of this species. Haplotypic diversity was highest in a small NSW subcatchment south of Evans Head (h = 0.594) followed by Marcus Creek in Queensland (h = 0.475). Distinct genetic differentiation was evident among the Queensland localities and the NSW subcatchments, implying restricted gene flow between coastal river systems. One of the nine haplotypes detected was distributed over 83.4% of the species’ range, suggesting historical connectivity among the now fragmented populations. These patterns were concordant with eustatic changes associated with the last glacial maximum. High barrier sand dunes may also act as barriers to gene flow and dispersal between adjacent NSW subcatchments. Conservation efforts should focus on the preservation of genetic diversity by maintaining as many genetically differentiated populations as possible. The relatively diverse populations inhabiting the South Evans Head subcatchment and Marcus Creek require special management consideration.

Genetic differentiation between estuarine and open coast ecotypes of a dominant ecosystem engineer

2019 ◽  
Vol 70 (7) ◽  
pp. 977 ◽  
Author(s):  
M. A. Coleman ◽  
J. S. Clark ◽  
M. A. Doblin ◽  
M. J. Bishop ◽  
B. P. Kelaher
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Ecosystem Engineer ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Random Mating ◽  
Rocky Shores ◽  
Open Coast ◽  
Key Species ◽  
Genetic Diversity And Structure

Temperate intertidal shores globally are often dominated by habitat-forming seaweeds, but our knowledge of these systems is heavily biased towards northern hemisphere species. Rocky intertidal shores throughout Australia and New Zealand are dominated by a single monotypic species, Hormosira banksii. This species plays a key role in facilitating biodiversity on both rocky shores and estuarine habitats, yet we know little about the processes that structure populations. Herein we characterise the genetic diversity and structure of Hormosira and demonstrate strong restrictions to gene flow over small spatial scales, as well as between estuarine and open coast populations. Estuarine ecotypes were often genetically unique from nearby open coast populations, possibly due to extant reduced gene flow between habitats, founder effects and coastal geomorphology. Deviations from random mating in many locations suggest complex demographic processes are at play within shores, including clonality in estuarine populations. Strong isolation by distance in Hormosira suggests that spatial management of intertidal habitats will necessitate a network of broad-scale protection. Understanding patterns of genetic diversity and gene flow in this important ecosystem engineer will enhance the ability to manage, conserve and restore this key species into the future.

Genetic diversity and structure in the northern populations of European hazelnut (Corylus avellana L.)

Genome ◽  
2019 ◽  
Vol 62 (8) ◽  
pp. 537-548
Author(s):  
Pirjo Tanhuanpää ◽  
Maarit Heinonen ◽  
Lidija Bitz ◽  
Veli-Matti Rokka
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Plant Conservation ◽  
Corylus Avellana ◽  
Ice Age ◽  
Genetic Structuring ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Genetic Diversity And Structure ◽  
Corylus Avellana L

European hazelnut (Corylus avellana L.) is a strictly cross-pollinated diploid tree species, which has its northernmost populations in Fennoscandia, and it was one of the first species to recolonize northern Europe after the last ice age. Hazelnut produces edible nuts in Finland but nowadays they are underutilized as food, and currently no breeding programmes exist. In the present study, 300 hazelnut specimens were collected from 20 different locations (= populations) in Finland, and they were genetically analyzed using nine simple sequence repeat (SSR) markers. Most of the genetic diversity existed within populations (83%). According to different genetic analyses (STRUCTURE, principal coordinates analysis, and clustering), a general lack of structure was observed, suggesting extensive gene flow among hazelnuts between 17 investigated populations. However, genetic structuring was clearly observed in three populations: Hakavuori, Mustiala, and Pähkinämäki, which might have become isolated due to geographical barriers that kept them separate, diminishing gene flow from other populations. Studying the diversity of European hazelnut is of great interest for understanding population genetics of a species distributed in its marginal areas in the north, and the results are also valuable for further uses in plant conservation, selection, and possible future breeding actions in Finland.

Genetic diversity and structure of the treeManilkara zapotain a naturally fragmented tropical forest

2017 ◽  
Vol 33 (4) ◽  
pp. 285-294 ◽  
Author(s):  
Daniela A. Martínez-Natarén ◽  
Víctor Parra-Tabla ◽  
Miguel A. Munguía-Rosas
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Tropical Forest ◽  
Isolation By Distance ◽  
Allelic Diversity ◽  
Long Distance ◽  
Population Genetic Differentiation ◽  
Continuous Forest ◽  
Genetic Diversity And Structure ◽  
Degree Of Isolation

Abstract:Forest fragmentation, habitat loss and isolation may have a strong effect on biodiversity in tropical forests. This can include modification of the genetic diversity and structure of plant populations. In this study, we assessed the genetic diversity and structure of the treeManilkara zapotain 15 naturally formed fragments of semi-evergreen tropical forest, as well as in an adjacent continuous forest for comparison. Forest fragments were scattered within a matrix of wetlands and were highly variable in terms of size and degree of isolation. The naturally fragmented populations ofM.zapotahad slightly less allelic diversity (Ar: 3.4) than those of the continuous forest (Ar: 3.6), when corrected for sample size. However, populations in the fragments and continuous forest had very similar heterozygosity levels (HE: 0.59 in both cases). Low levels of genetic differentiation were observed among populations (FST: 0.026) and genetic structure was not consistent with isolation by distance, indicating high levels of gene flow. Genetic diversity was not explained by fragment size or degree of isolation. The relatively high genetic diversity and low inter-population genetic differentiation observed inM. zapotamay be the result of long-distance pollen and seed dispersal, as well as the high proximity among patches.

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