scholarly journals Genetic diversity, genetic structure and phylogeography of the Iberian endemicGypsophila struthium(Caryophyllaceae) as revealed by AFLP and plastid DNA sequences: connecting habitat fragmentation and diversification

2013 ◽  
Vol 173 (4) ◽  
pp. 654-675 ◽  
Author(s):  
María Isabel Martínez-Nieto ◽  
José Gabriel Segarra-Moragues ◽  
Encarnación Merlo ◽  
Fabián Martínez-Hernández ◽  
Juan Francisco Mota
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Dna Sequences ◽  
Plastid Dna

scholarly journals Genetic structure and diversity of the endangered growling grass frog in a rapidly urbanizing region

2015 ◽  
Vol 2 (8) ◽  
pp. 140255 ◽  
Author(s):  
Claire C. Keely ◽  
Joshua M. Hale ◽  
Geoffrey W. Heard ◽  
Kirsten M. Parris ◽  
Joanna Sumner ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Urban Expansion ◽  
Nuclear Gene ◽  
Management Approach ◽  
Natural Habitats ◽  
High Genetic Diversity ◽  
Genetic Structure And Diversity

Two pervasive and fundamental impacts of urbanization are the loss and fragmentation of natural habitats. From a genetic perspective, these impacts manifest as reduced genetic diversity and ultimately reduced genetic viability. The growling grass frog ( Litoria raniformis ) is listed as vulnerable to extinction in Australia, and endangered in the state of Victoria. Remaining populations of this species in and around the city of Melbourne are threatened by habitat loss, degradation and fragmentation due to urban expansion. We used mitochondrial DNA (mtDNA) and microsatellites to study the genetic structure and diversity of L. raniformis across Melbourne's urban fringe, and also screened four nuclear gene regions (POMC, RAG-1, Rhod and CRYBA1). The mtDNA and nuclear DNA sequences revealed low levels of genetic diversity throughout remnant populations of L. raniformis . However, one of the four regions studied, Cardinia, exhibited relatively high genetic diversity and several unique haplotypes, suggesting this region should be recognized as a separate Management Unit. We discuss the implications of these results for the conservation of L. raniformis in urbanizing landscapes, particularly the potential risks and benefits of translocation, which remains a contentious management approach for this species.

scholarly journals First regional evaluation of nuclear genetic diversity and population structure in northeastern coyotes (Canis latrans)

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 66 ◽  
Author(s):  
Javier Monzón
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Molecular Markers ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Canis Latrans ◽  
Regional Analysis ◽  
Model Organism ◽  
Nucleotide Polymorphisms ◽  
Genomic Markers

Previous genetic studies of eastern coyotes (Canis latrans) are based on one of two strategies: sampling many individuals using one or very few molecular markers, or sampling very few individuals using many genomic markers. Thus, a regional analysis of genetic diversity and population structure in eastern coyotes using many samples and several molecular markers is lacking. I evaluated genetic diversity and population structure in 385 northeastern coyotes using 16 common single nucleotide polymorphisms (SNPs). A region-wide analysis of population structure revealed three primary genetic populations, but these do not correspond to the same three subdivisions inferred in a previous analysis of mitochondrial DNA sequences. More focused geographic analyses of population structure indicated that ample genetic structure occurs in coyotes from an intermediate contact zone where two range expansion fronts meet. These results demonstrate that genotyping several highly heterozygous SNPs in a large, geographically dense sample is an effective way to detect cryptic population genetic structure. The importance of SNPs in studies of population and wildlife genomics is rapidly increasing; this study adds to the growing body of recent literature that demonstrates the utility of SNPs ascertained from a model organism for evolutionary inference in closely related species.

Molecular phylogeny and genetic diversity of genus Capparis (Capparaceae) based on plastid DNA sequences and ISSR markers

2017 ◽  
Vol 304 (2) ◽  
pp. 205-217 ◽  
Author(s):  
Asif S. Tamboli ◽  
Pradnya B. Yadav ◽  
Aatiya A. Gothe ◽  
Shrirang R. Yadav ◽  
Sanjay P. Govindwar
Keyword(s):  
Genetic Diversity ◽  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Plastid Dna ◽  
Issr Markers

scholarly journals Mitochondrial DNA sequence variations in populations of Sardinapilchardus(Walbaum 1792) along the Tunisian coasts

2019 ◽  
Vol 20 (2) ◽  
Author(s):  
ΚARIMA FADHLAOUI-ZID
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Structure ◽  
Dna Sequences ◽  
Population Distribution ◽  
Genetic Structuring ◽  
Efficient Management ◽  
Sequence Variations ◽  
Haplotypic Diversity ◽  
High Level

Sardine is a fish species of great economic importance to Tunisia. Knowledge of genetic diversity and population distribution is essential for an efficient management and sustainability of any regional fishery. This study aimed to assessing the genetic structure and to specify the stocks of the European sardine (Sardina pilchardus). To this end, 83 specimens were collected from three localities along the Tunisian coast and analysed using mitochondrial DNA sequences. The results of sequence analysis determined the existence of variations in 40 single nucleotide sites within the 307 bp fragment of the cytb gene examined and defined twenty different haplotypes. Genetic diversity, estimated by haplotypic diversity, was high in all samples. Tunisian S.pilchardus samples show some level of genetic structuring. First, genetic differentiation between localities (ΦST estimates) was significant for all comparison. Second, the analysis of molecular variance AMOVA indicates a high level of genetic variation (ΦST = 0.093; P<0.001). The structural patterns identified can be explained largely in relation to the regional oceanographic features. In conclusion, this study provided initial genetic data in making inference of the genetic structure of S. pilchardus along the Tunisian coasts. 

scholarly journals ddRAD Sequencing: A Novel Arsenal Added to the Biosecurity Toolbox to Trace the Origin of Brown Marmorated Stink Bug, Halyomorpha Halys (Hemiptera: Pentatomidae)

2020 ◽  
Author(s):  
Juncong Yan ◽  
Gábor Vétek ◽  
Chandan Pal ◽  
Jinping Zhang ◽  
Rania Gmati ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Dna Sequences ◽  
Insect Pest ◽  
Economic Losses ◽  
Halyomorpha Halys ◽  
Invasion History ◽  
Stink Bug ◽  
Genetic Clusters

Abstract BackgroundBrown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. It is a polyphagous insect pest and causing significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance.ResultA total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters. ConclusionThe study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also separated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating from multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance knowledge of genetic diversity among BMSB populations and demonstrate a great potential to trace the origin of BMSB individuals for future invasion events.

scholarly journals Genome-wide SNPs Detect Fine-scale Genetic Structure in Threatened Populations of Squirrel Glider Petaurus Norfolcensis

2021 ◽  
Author(s):  
Monica Knipler ◽  
Mark Dowton ◽  
John Clulow ◽  
Ninon Meyer ◽  
Katarina M. Mikac
Keyword(s):  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Species Conservation ◽  
Population Declines ◽  
Least Cost Path ◽  
South Wales ◽  
Genome Wide ◽  
Squirrel Glider

Abstract Australian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,812 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.

scholarly journals Genetic variation and genetic structure within metapopulations of two closely related selfing and outcrossing Zingiber species (Zingiberaceae)

AoB Plants ◽  
2020 ◽  
Author(s):  
Rong Huang ◽  
Zong-Dian Zhang ◽  
Yu Wang ◽  
Ying-Qiang Wang
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Spatial Genetic Structure ◽  
Full Range ◽  
Breeding Systems ◽  
Dispersal Ability ◽  
Phylogenetic Distance ◽  
Plant Populations

Abstract Habitat fragmentation strongly affects the genetic diversity of plant populations, and this has always attracted much research interest. Although numerous studies have investigated the effects of habitat fragmentation on the genetic diversity of plant populations, fewer studies have compared species with contrasting breeding systems while accounting for phylogenetic distance. Here, we compare the levels of genetic diversity and differentiation within and among subpopulations in metapopulations (at fine-scale level) of two closely related Zingiber species, selfing Zingiber corallinum and outcrossing Zingiber nudicarpum. Comparisons of the genetic structure of species from unrelated taxa may be confounded by the effects of correlated ecological traits or/and phylogeny. Thus, we possibly reveal the differences in genetic diversity and spatial distribution of genetic variation within metapopulations that relate to mating systems. Compared to outcrossing Z. nudicarpum, the subpopulation genetic diversity in selfing Z. corallinum was significantly lower, but the metapopulation genetic diversity was not different. Most genetic variation resided among subpopulations in selfing Z. corallinum metapopulations, while a significant portion of variation resided either within or among subpopulations in outcrossing Z. nudicarpum, depending on whether the degree of subpopulation isolation surpass the dispersal ability of pollen and seed. A stronger spatial genetic structure appeared within subpopulations of selfing Z. corallinum potentially due to restricted pollen flow and seed dispersal. In contrast, a weaker genetic structure was apparent in subpopulations of outcrossing Z. nudicarpum most likely caused by extensive pollen movement. Our study shows that high genetic variation can be maintained within metapopulations of selfing Zingiber species, due to increased genetic differentiation intensified primarily by the stochastic force of genetic drift among subpopulations. Therefore, maintenance of natural variability among subpopulations in fragmented areas is key to conserve the full range of genetic diversity of selfing Zingiber species. For outcrossing Zingiber species, maintenance of large populations is an important factor to enhance genetic diversity.

scholarly journals Genetic diversity and population structure of the endangered basal angiospermBrasenia schreberi(Cabombaceae) in China

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5296 ◽  
Author(s):  
Zhi-Zhong Li ◽  
Andrew W. Gichira ◽  
Qing-Feng Wang ◽  
Jin-Ming Chen
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Glacial Refugia ◽  
Mantel Test ◽  
Ex Situ ◽  
Brasenia Schreberi ◽  
Genetic Diversity And Structure ◽  
Rare And Endangered

Brasenia schreberiJ.F. Gmelin (Cabombaceae), an aquatic herb that occurs in fragmented locations in China, is rare and endangered. Understanding its genetic diversity and structure is crucial for its conservation and management. In this study, 12 microsatellite markers were used to estimate the genetic diversity and variation in 21 populations ofB. schreberiin China. A total of 61 alleles were found; assessment of allelic richness (Ar = 1.92) and observed and expected heterozygosity (HO= 0.200,HE= 0.256) suggest lower genetic diversity compared to some endangered species, and higher variation was observed within populations (58.68%) rather than among populations (41.32%). No significant correlation between geographical and genetic distance among populations was detected (Mantel test,r= 0.0694;P= 0.7985), which may have likely resulted from barriers to gene flow (Nm = 0.361) that were produced by habitat fragmentation. However, Bayesian and neighbor-joining cluster analyses suggest a population genetic structure consisting of two clusters (I and II) or four subclusters (I-1, 2 and II-1, 2). The genetic structure and distribution ofB. schreberiin China may have involved glacial refugia that underwent range expansions, introgression, and habitat fragmentation. The findings of the present study emphasize the importance for both in situ and ex situ conservation efforts.

scholarly journals The effects of habitat fragmentation on the genetic structure of wild boar (Sus scrofa) population in Lithuania

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Loreta Griciuvienė ◽  
Žygimantas Janeliūnas ◽  
Vaclovas Jurgelevičius ◽  
Algimantas Paulauskas
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Habitat Fragmentation ◽  
Wild Boar ◽  
Sus Scrofa ◽  
Isolation By Distance ◽  
Wild Boar Population ◽  
Ecological Features

Abstract Background Wild boar (Sus scrofa) is a widely distributed ungulate whose success can be attributed to a variety of ecological features. The genetic variation and population structure of Lithuania’s wild boar population have not yet been thoroughly studied. The purposes of this study were to investigate the genetic diversity of S. scrofa and assess the effects of habitat fragmentation on the population structure of wild boar in Lithuania. A total of 96 S. scrofa individuals collected from different regions of Lithuania were genotyped using fifteen microsatellite loci. Results The microsatellite analysis of the wild boars indicated high levels of genetic diversity within the population. Microsatellite markers showed evidence of a single panmictic wild boar population in Lithuania according to STRUCTURE’s highest average likelihood, which was K = 1. This was supported by pairwise Fst values and AMOVA, which indicated no differentiation between the four sampling areas. The results of the Mantel test revealed a weak isolation by distance and geographic diversity gradients that persisted between locations. Motorway fencing and heavy traffic were not an effective barrier to wild boar movement. Conclusions There was limited evidence of population genetic structure among the wild boar, supporting the presence of a single population across the study area and indicating that there may be no barriers hindering wild boar dispersal across the landscape. The widespread wild boar population in Lithuania, the high level of genetic variation observed within subpopulations, and the low level of variation identified between subpopulations suggest migration and gene flow between locations. The results of this study should provide valuable information in future for understanding and comparing the detailed structure of wild boar population in Lithuania following the outbreak of African swine fever.

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