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.

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 Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0255418
Author(s):  
Siou Ting Gan ◽  
Chin Jit Teo ◽  
Shobana Manirasa ◽  
Wei Chee Wong ◽  
Choo Kien Wong
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Oil Palm ◽  
Core Collection ◽  
Elaeis Guineensis ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Fixation Index ◽  
Core Set ◽  
Genetic Diversity And Structure

Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright’s fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei’s genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.

scholarly journals Genetic Structure and Relationships among Wild and Cultivated Grapevines from Central Europe and Part of the Western Balkan Peninsula

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 962
Author(s):  
Goran Zdunić ◽  
Katarina Lukšić ◽  
Zora Annamaria Nagy ◽  
Ana Mucalo ◽  
Katarina Hančević ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Central Europe ◽  
Balkan Peninsula ◽  
Gene Pools ◽  
Natural Habitats ◽  
Central European ◽  
Genetic Diversity And Structure ◽  
Wild Grapevine ◽  
Western Balkan Region ◽  
Balkan Region

The genetic diversity and relationship between wild (Vitis vinifera L. subsp. sylvestris (Gmel.) Hegi and cultivated (V. vinifera L. subsp. vinifera) grapevine in the western Balkan region and Central Europe have not been studied together previously, although this area has a rich viticultural past. Here, we studied wild grapevine populations sampled from their natural habitats in several countries of the western Balkan region and Central Europe. Their genetic diversity and structure were compared to cultivars that are traditionally in use in this region. A sample set of 243 accessions was genotyped at 20 nuclear microsatellite loci, including 167 sylvestris and 76 diverse vinifera cultivars. The genetic diversity of the wild grapevines was lower than that of cultivars by all genetic parameters. Both hierarchical and nonhierarchical clustering methods differentiated two main groups, indicating clear separation between wild and cultivated vines but also revealed clear gene flow between the cultivated and wild gene pools through overlaps and admixed ancestry values in the graphs. There was greater affinity to the wild grapes in Central European cultivars than in Balkan cultivars. Fine arrangement of the structure among cultivated grapevines showed differentiation among Central European and Balkan cultivars. These results confirm the divergence of wild grapes from vinifera and highlight the “crossroad” role of the western Balkan peninsula in the broader context of European viticulture.

scholarly journals Low Genetic Diversity of Declining Viola uliginosa (Violaceae) at its Southern Range Limits in Poland

2016 ◽  
Vol 58 (2) ◽  
pp. 71-82 ◽  
Author(s):  
Wojciech Paul ◽  
Elżbieta Cieślak ◽  
Michał Ronikier ◽  
Grzegorz Migdałek ◽  
Aneta Słomka ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Isolation By Distance ◽  
Distinct Group ◽  
Mantel Test ◽  
Natural Habitats ◽  
Protection Measures ◽  
Red Lists ◽  
Low Genetic Diversity ◽  
Declining Species

AbstractViola uliginosa(bog violet) is a declining species throughout its range due to – mostly anthropogenic – drying out of the wet habitats it occupies. Using AFLP markers, we aimed to estimate the genetic diversity in Polish populations, that may give an insight into the situation of plant populations facing rapid loss of natural habitats.Bog violet from several dispersed Polish populations is generally characterized by very low genetic diversity (HT= 0.048), even lower than several other endangered violets; therefore, we suggest that it should preserve at least EN rank in the red lists/red data books. The mean gene diversity within all populations (HS) was much lower than gene diversity (GST) between populations (0.020 versus 0.583, respectively) which supports the prevalence of clonal propagation of the species (mainly by stolons) but may also point to some significance of autogamy in cleisto- and chasmogamous flowers. A highFSTvalue and the Mantel test for all populations revealed significant isolation by distance. Geographically neighboring pairs of populations formed genetic clusters supported by all (in the case of two closest populations) or most statistical analyses applied. Special attention should be paid to thelocus classicusof the species in Rząska, consisting of a small number of individuals, forming a genetically distinct group, revealing very low gene diversity (Hj= 0.009) and the longest genetic distance to the remaining populations. Our results can contribute to planning future protection measures for the species at this and other locations. Genetic structure of the studied populations suggests local affinities of populations but does not generally support hypothesized recent continuity ofV. uliginosarange along the river valleys of southern Poland; this view may, however, be altered with widening of the scope of studied populations and chosen molecular markers.

scholarly journals Clinging to survival: Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum persists in shrinking forest patches

Oryx ◽  
2021 ◽  
pp. 1-6
Author(s):  
Krystal A. Tolley ◽  
Colin R. Tilbury ◽  
Jessica M. da Silva ◽  
Gary Brown ◽  
Yankho Chapeta ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Satellite Imagery ◽  
Critically Endangered ◽  
Forest Loss ◽  
Mitochondrial Marker ◽  
Forest Patches ◽  
Genetic Diversity And Structure ◽  
The Impact

Abstract The Critically Endangered Chapman's pygmy chameleon Rhampholeon chapmanorum is endemic to the low elevation rainforest of the Malawi Hills in southern Malawi. Much of this forest has been converted to agriculture and it was uncertain whether chameleon populations have persisted. We used current and historical satellite imagery to identify remaining forest patches and assess deforestation. We then surveyed forest patches for the presence of this chameleon, and assessed its genetic diversity and structure. We estimated that 80% of the forest has been destroyed since 1984, although we found extant populations of the chameleon in each of the patches surveyed. Differentiation of genetic structure was strong between populations, suggesting that gene flow has been impaired. Genetic diversity was not low, but this could be the result of a temporal lag as well as lack of sensitivity in the mitochondrial marker used. Overall, the impact of forest loss is assumed to have led to a large demographic decline, with forest fragmentation preventing gene flow.

scholarly journals Genetic diversity and species identity of the critically endangered Rote Island snake-necked turtle, Chelodina mccordi Rhodin, 1994

2021 ◽  
Vol 948 (1) ◽  
pp. 012001
Author(s):  
N A Devi ◽  
R Eprilurahman ◽  
D S Yudha ◽  
S Raharjo ◽  
M As-Singkily ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Dna Sequences ◽  
Captive Breeding ◽  
Haplotype Diversity ◽  
Genetic Distances ◽  
Ex Situ ◽  
Species Identity ◽  
Natural Habitats ◽  
Diversity Assessment

Abstract The endemic Chelodina mccordi is considered extinct in the wild; however, ex-situ populations are thriving and sampled for our genetic diversity assessment. We used three sequences resulting from blood and tissue samples of five individual turtles amplified for 650-bp cytochrome oxidase I (COI) fragment of the mitochondrial DNA. We analysed a total of 30 barcoding DNA sequences for phylogenetic relationships and genetic distances among Chelodina spp. Nucleotide diversity of eight C. mccordi samples is 0.007 ± 0.001 with a haplotype diversity of 0.893 ± 0.086. All these samples form a monophyletic clade that is sister to a clade of Australian and New Guinean long-necked turtles. Genetic distances calculated using Kimura 2-paramater model among C. mccordi sequences range between 0.2% and 1.5%, while a few others are without distance. The shortest genetic distance is between individuals from Rote Island, whereas the longest distance was found between individuals, each of which was derived from parental stocks originating in Rote and Timor islands. A genetic distance of 1.1% - 1.5% is likely to denote distinction at subspecies level. Results of this study could help in reintroducing captive individuals into their natural habitats. Thus, captive breeding programme of this species may help its conservation.

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 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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