High nuclear genetic differentiation, but low chloroplast diversity in a rare species, Aluta quadrata (Myrtaceae), with a disjunct distribution in the Pilbara, Western Australia

2016 ◽  
Vol 64 (8) ◽  
pp. 687 ◽  
Author(s):  
M. Byrne ◽  
D. J. Coates ◽  
B. M. Macdonald ◽  
M. Hankinson ◽  
S. M. McArthur ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Microsatellite Loci ◽  
Disjunct Distribution ◽  
Chloroplast Gene ◽  
Seed Sources ◽  
Chloroplast Haplotype ◽  
Haplotype Variation

Geographically separated populations may show high levels of genetic differentiation, depending on the levels of current and historical isolation. In the ancient landscape of the Pilbara region, there are few plant species with restricted distributions, and one such species, Aluta quadrata Rye & Trudgen, is restricted to three separate locations on the southern edge of the Hamersley Range. We investigated genetic diversity and differentiation among geographically isolated locations of A. quadrata, using 10 microsatellite loci to assess contemporary genetic structure, and sequences of seven chloroplast gene regions to infer historical isolation. Nuclear genetic diversity was moderate, with moderate to high genetic differentiation among the three locations, and low differentiation among populations within locations. In contrast, there was no detected variation in the chloroplast genome. The high genetic differentiation is consistent with limited contemporary connectivity among the geographically separated locations, although lack of chloroplast haplotype variation indicates that limited connectivity has occurred more recently and is not due to historical isolation. The level of differentiation suggests use of local seed sources for augmentation or establishment of populations within gene flow distance of existing populations, whereas an experimental translocation established on more distant sites could use mixed seed sources to maximise genetic diversity.

scholarly journals Variation and genetic structure of the endangered Lepus flavigularis (Lagomorpha: Leporidae)

2017 ◽  
Vol 65 (4) ◽  
pp. 1322
Author(s):  
Bárbara Cruz Salazar ◽  
Consuelo Lorenzo ◽  
Eduardo Espinoza Medinilla ◽  
Sergio López
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
San Francisco ◽  
Isolation By Distance ◽  
Santa Cruz ◽  
Management Units ◽  
Lepus Flavigularis ◽  
Santa Maria

Lepus flavigularis, is an endemic and endangered species, with only four populations inhabiting Oaxaca, México: Montecillo Santa Cruz, Aguachil, San Francisco del Mar Viejo and Santa María del Mar. Nevertheless, human activities like poaching and land use changes, and the low genetic diversity detected with mitochondrial DNA and allozymes in previous studies, have supported the urgent need of management strategies for this species, and suggest the definition of management units. For this, it is necessary to study the genetic structure with nuclear genes, due to their inheritance and high polymorphism, therefore, the objective of this study was to examine the variation and genetic structure of L. flavigularis using nuclear microsatellites. We sampled four populations of L. flavigularis and a total of 67 jackrabbits were captured by night sampling during the period of 2001 to 2006. We obtained the genomic DNA by the phenol-chloroform-isoamyl alcohol method. To obtain the diversity and genetic structure, seven microsatellites were amplified using the Polymerase Chain Reaction (PCR); the amplifications were visualized through electrophoresis with 10 % polyacrylamide gels, dyed with ethidium bromide. Genetic diversity was determined using the software GenAlEx v. 6.4, and genetic structure was obtained with ARLEQUIN v. 3.1; null alleles were evaluated using the program Micro-Checker v.2.2.2. Additionally, a Bayesian analysis was performed with software STRUCTURE v. 2.2.3., and the isolation by distance (IBD) was studied using the program PASSAGE v.2.0.11.6. Our results showed that the genetic variation found was low (HO = 0.30, HE = 0.24) when compared to other jackrabbit species. Fixed alleles and moderate levels of genetic differentiation (FST = 0.18, P = 0.001) were detected among populations, indicating the effect of the genetic drift and limited gene flow. Bayesian clustering analysis revealed two groups: (1) jackrabbits from Montecillo Santa Cruz, and (2) individuals living in Aguachil, San Francisco del Mar Viejo and Santa María del Mar. No evidence was found of isolation by distance. It is possible that the geographic barriers present between populations (e.g. lagoons, human settlements), rather than the geographical distance between them, may explain the observed genetic structure. The inbreeding coefficient was negative (FIS = -0.27, P = 0.03), indicating genetic sub-structure in populations. We suggest two management units based on the genetically closer populations, which will help define precise conservation actions in L. flavigularis. This research is the basis for defining translocation of individuals between populations, nevertheless, a more extensive future study, with specific molecular markers for L. flavigularis, is required. In addition, it is necessary to analyze the barriers that limit the gene flow, since it is urgent to reduce the genetic differentiation between populations and increase the genetic diversity of this species. 

scholarly journals Genetic Diversity and Population Structure in the Ryukyu Flying Fox Inferred from Remote Sampling in the Yaeyama Archipelago

2020 ◽  
Author(s):  
Yuto Taki ◽  
Christian E. Vincenot ◽  
Yu Sato ◽  
Miho Inoue-Murayama
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Haplotype Network ◽  
Iucn Red List ◽  
The Philippines ◽  
Conservation Units ◽  
Long Distance ◽  
Flying Fox

AbstractThe Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. Although P. dasymallus is listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species.mtDNA analysis was conducted with 142 DNA remote samples, mostly from feces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure.Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population.We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among populations of the archipelago. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

scholarly journals Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

2012 ◽  
Vol 93 (6) ◽  
pp. 1512-1524 ◽  
Author(s):  
Sarah A. Sonsthagen ◽  
Chadwick V. Jay ◽  
Anthony S. Fischbach ◽  
George K. Sage ◽  
Sandra L. Talbot
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Spatial Genetic Structure ◽  
Genetic Relationships ◽  
Breeding Population ◽  
Pacific Walrus ◽  
Breeding Populations ◽  
The Pacific

Abstract Pacific walruses (Odobenus rosmarus divergens) occupying shelf waters of Pacific Arctic seas migrate during spring and summer from 3 breeding areas in the Bering Sea to form sexually segregated nonbreeding aggregations. We assessed genetic relationships among 2 putative breeding populations and 6 nonbreeding aggregations. Analyses of mitochondrial DNA (mtDNA) control region sequence data suggest that males are distinct among breeding populations (ΦST = 0.051), and between the eastern Chukchi and other nonbreeding aggregations (ΦST = 0.336–0.449). Nonbreeding female aggregations were genetically distinct across marker types (microsatellite FST = 0.019; mtDNA ΦST = 0.313), as was eastern Chukchi and all other nonbreeding aggregations (microsatellite FST = 0.019–0.035; mtDNA ΦST = 0.386–0.389). Gene flow estimates are asymmetrical from St. Lawrence Island into the southeastern Bering breeding population for both sexes. Partitioning of haplotype frequencies among breeding populations suggests that individuals exhibit some degree of philopatry, although weak. High levels of genetic differentiation among eastern Chukchi and all other nonbreeding aggregations, but considerably lower genetic differentiation between breeding populations, suggest that at least 1 genetically distinct breeding population remained unsampled. Limited genetic structure at microsatellite loci between assayed breeding areas can emerge from several processes, including male-mediated gene flow, or population admixture following a decrease in census size (i.e., due to commercial harvest during 1880–1950s) and subsequent recovery. Nevertheless, high levels of genetic diversity in the Pacific walrus, which withstood prolonged decreases in census numbers with little impact on neutral genetic diversity, may reflect resiliency in the face of past environmental challenges.

scholarly journals Genetic diversity of Dactylorhiza incarnata (Orchidaceae) in northern Poland

2016 ◽  
Vol 85 (2) ◽  
Author(s):  
Aleksandra M. Naczk ◽  
Igor J. Chybicki ◽  
Marek S. Ziętara
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Pollen Dispersal ◽  
Species Level ◽  
Bottleneck Effect ◽  
Northern Poland ◽  
Habitat Loss And Fragmentation ◽  
Population Numbers

The genetic structure of <em>Dactylorhiza incarnata</em> var. <em>incarnata</em> populations is shaped not only by historical events such as recolonization after ice sheet retreat or limited seed and pollen dispersal, but also the bottleneck effect. During the last decade, <em>D. incarnata</em> var. <em>incarnata</em> has also experienced a strong decline in population numbers and sizes, due to habitat loss and fragmentation. In the present research genetic diversity was examined in eight populations located in northern Poland, using six nuclear microsatellites loci. At the species level our results showed a moderate mean level of genetic diversity (<em>A</em> = 4.67; <em>A</em><span><sub>e</sub></span> = 2.73; <em>R</em><span><sub>s</sub></span> = 4.48; <em>H</em><span><sub>o</sub></span> = 0.438; <em>F</em><span><sub>IS</sub></span> = 0.224), which varied among the studied populations (<em>A</em>: 2.17–3.67; <em>A</em><span><sub>e</sub></span>: 1.55–2.69; <em>R</em><span><sub>s</sub></span>: 1.31–1.61; <em>H</em><span><sub>o</sub></span>: 0.292–0.631; <em>F</em><span><sub>IS</sub></span>: −0.283–0.340). A considerable overabundance of homozygotes was detected in four populations (<em>F</em><span><sub>IS</sub></span> within the range of 0.067–0.340), and in the remaining populations an excess of heterozygotes was observed. The average apparent out-crossing rate was also calculated (<em>t</em><span><sub>a</sub></span> = 0.980), and primarily indicated a tendency to out-cross within the species. Moderate genetic differentiation was found among the studied populations (<em>F</em><span><sub>ST</sub></span> = 0.149; <em>R</em><span><sub>ST</sub></span> = 0.174; <em>p</em> &lt; 0.05). The differentiation of the populations corresponded to relatively low gene flow value (<em>N</em><span><sub>m</sub></span> = 0.426) among populations, which amounted to only one migrant every second generation.

scholarly journals Weak population spatial genetic structure and low infraspecific specificity for fungal partners in the rare mycoheterotrophic orchid Epipogium aphyllum

2022 ◽  
Author(s):  
Julita Minasiewicz ◽  
Emilia Krawczyk ◽  
Joanna Znaniecka ◽  
Lucie Vincenot ◽  
Ekaterina Zheleznaya ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Plastid Dna ◽  
Nuclear Microsatellites ◽  
Nuclear Ribosomal Dna ◽  
Genetic Characteristics ◽  
Mycorrhizal Specificity ◽  
Mycoheterotrophic Plants

AbstractSome plants abandoned photosynthesis and developed full dependency on fungi for nutrition. Most of the so-called mycoheterotrophic plants exhibit high specificity towards their fungal partners. We tested whether natural rarity of mycoheterotrophic plants and usual small and fluctuating population size make their populations more prone to genetic differentiation caused by restricted gene flow and/or genetic drift. We also tested whether these genetic characteristics might in turn shape divergent fungal preferences. We studied the mycoheterotrophic orchid Epipogium aphyllum, addressing the joint issues of genetic structure of its populations over Europe and possible consequences for mycorrhizal specificity within the associated fungal taxa. Out of 27 sampled E. aphyllum populations, nine were included for genetic diversity assessment using nine nuclear microsatellites and plastid DNA. Population genetic structure was inferred based on the total number of populations. Individuals from 17 locations were included into analysis of genetic identity of mycorrhizal fungi of E. aphyllum based on barcoding by nuclear ribosomal DNA. Epipogium aphyllum populations revealed high genetic diversity (uHe = 0.562) and low genetic differentiation over vast distances (FST = 0.106 for nuclear microsatellites and FST = 0.156 for plastid DNA). Bayesian clustering analyses identified only two genetic clusters, with a high degree of admixture. Epipogium aphyllum genets arise from panmixia and display locally variable, but relatively high production of ramets, as shown by a low value of rarefied genotypic richness (Rr = 0.265). Epipogium aphyllum genotype control over partner selection was negligible as (1) we found ramets from a single genetic individual associated with up to 68% of the known Inocybe spp. associating with the plant species, (2) and partner identity did not show any geographic structure. The absence of mosaicism in the mycorrhizal specificity over Europe may be linked to preferential allogamous habit of E. aphyllum and significant gene flow, which tend to promote host generalism.

scholarly journals Genetic diversity and population structure in the Ryukyu flying fox inferred from remote sampling in the Yaeyama archipelago

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248672
Author(s):  
Yuto Taki ◽  
Christian E. Vincenot ◽  
Yu Sato ◽  
Miho Inoue-Murayama
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Haplotype Network ◽  
Iucn Red List ◽  
The Philippines ◽  
Conservation Units ◽  
Long Distance ◽  
Flying Fox

The Ryukyu flying fox (Pteropus dasymallus) is distributed throughout the island chain spanning across southern Japan, Taiwan, and possibly the Philippines. AlthoughP.dasymallusis listed as VU (vulnerable) in the IUCN Red List, only few genetic works have been conducted to support its conservation. In this study we analyzed 19 markers (mtDNA haplotypes and 18 microsatellite markers) to evaluate genetic diversity and investigate the genetic structure of this species. mtDNA analysis was conducted with 142 DNA remote samples, mostly from faeces, and wing tissues collected on eight islands (Miyako, Ishigaki, Kohama, Kuroshima, Hateruma, Taketomi, Iriomote, Yonaguni). 39 haplotypes were identified in 526bp of the control region, and haplotype network showed no clear genetic structure. Microsatellite analysis was also conducted with 155 samples collected on six islands (Miyako, Ishigaki, Kohama, Taketomi, Iriomote, Yonaguni). It showed that the Yonaguni population exhibits low genetic diversity, high inbreeding, and clear genetic differentiation from other populations. Gene flow between Ishigaki and Miyako through small stepstone islands might be preventing inbreeding of the Miyako population. We provide for the first time indirect proof of long-distance inter-island dispersal in the Ryukyu flying fox and revealed genetic diversity, gene flow and genetic differentiation among the archipelago’s populations. These results will be useful for delineating conservation units and designing specific conservation policies for each island based on metapopulation genetic structure.

Genetic diversity and population structure of Korean alder (Alnus japonica; Betulaceae)

1999 ◽  
Vol 29 (9) ◽  
pp. 1311-1316 ◽  
Author(s):  
Man Kyu Huh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Alnus Japonica ◽  
Alnus Crispa ◽  
The Mean ◽  
Fixation Indices

The genetic diversity and population genetic structure of Alnus japonica (Thunb.) Steudel in Korea were studied and compared with those of alder from Canada. Nineteen of the 25 loci studied (76.0%) showed detectable polymorphism. The mean genetic diversity within populations was 0.207, which was higher than that for two Canadian alder species (Alnus rugosa (Du Roi) Spreng. and Alnus crispa (Ait.) Pursh). Analysis of fixation indices, calculated for all polymorphic loci in each population, showed a substantial deficiency of heterozygotes relative to Hardy-Weinberg expectations. The mean population differentiation value of A. japonica in Korea (GST = 0.095) is similar to those of A. rugosa in Canada (GST = 0.052). These low values of GST in two countries, reflecting little spatial genetic differentiation, may indicate extensive gene flow (via pollen and (or) seeds) and (or) recent colonization.

scholarly journals Patterns of spatial genetic structures in Aedes albopictus (Diptera: Culicidae) populations in China

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Yong Wei ◽  
Jiatian Wang ◽  
Zhangyao Song ◽  
Yulan He ◽  
Zihao Zheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Spatial Genetic Structure ◽  
Vector Borne Diseases ◽  
Vector Borne ◽  
Genetic Structures

Abstract Background The Asian tiger mosquito, Aedes albopictus, is one of the 100 worst invasive species in the world and the vector for several arboviruses including dengue, Zika and chikungunya viruses. Understanding the population spatial genetic structure, migration, and gene flow of vector species is critical to effectively preventing and controlling vector-borne diseases. Little is known about the population structure and genetic differentiation of native Ae. albopictus in China. The aim of this study was to examine the patterns of the spatial genetic structures of native Ae. albopictus populations, and their relationship to dengue incidence, on a large geographical scale. Methods During 2016–2018, adult female Ae. albopictus mosquitoes were collected by human landing catch (HLC) or human-bait sweep-net collections in 34 localities across China. Thirteen microsatellite markers were used to examine the patterns of genetic diversity, population structure, and gene flow among native Ae. albopictus populations. The correlation between population genetic indices and dengue incidence was also examined. Results A total of 153 distinct alleles were identified at the 13 microsatellite loci in the tested populations. All loci were polymorphic, with the number of distinct alleles ranging from eight to sixteen. Genetic parameters such as PIC, heterozygosity, allelic richness and fixation index (FST) revealed highly polymorphic markers, high genetic diversity, and low population genetic differentiation. In addition, Bayesian analysis of population structure showed two distinct genetic groups in southern-western and eastern-central-northern China. The Mantel test indicated a positive correlation between genetic distance and geographical distance (R2 = 0.245, P = 0.01). STRUCTURE analysis, PCoA and GLS interpolation analysis indicated that Ae. albopictus populations in China were regionally clustered. Gene flow and relatedness estimates were generally high between populations. We observed no correlation between population genetic indices of microsatellite loci in Ae. albopictus populations and dengue incidence. Conclusion Strong gene flow probably assisted by human activities inhibited population differentiation and promoted genetic diversity among populations of Ae. albopictus. This may represent a potential risk of rapid spread of mosquito-borne diseases. The spatial genetic structure, coupled with the association between genetic indices and dengue incidence, may have important implications for understanding the epidemiology, prevention, and control of vector-borne diseases.

scholarly journals Genetic diversity in Tunisian horse breeds

2017 ◽  
Vol 60 (2) ◽  
pp. 153-160 ◽  
Author(s):  
Bayrem Jemmali ◽  
Mohamed Mezir Haddad ◽  
Nawel Barhoumi ◽  
Syrine Tounsi ◽  
Faten Lasfer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Microsatellite Loci ◽  
Genomic Dna ◽  
Genetic Distances ◽  
Jugular Veins ◽  
Blood Samples ◽  
Important Amount

Abstract. This study aimed at screening genetic diversity and differentiation in four horse breeds raised in Tunisia, the Barb, Arab-Barb, Arabian, and English Thoroughbred breeds. A total of 200 blood samples (50 for each breed) were collected from the jugular veins of animals, and genomic DNA was extracted. The analysis of the genetic structure was carried out using a panel of 16 microsatellite loci. Results showed that all studied microsatellite markers were highly polymorphic in all breeds. Overall, a total of 147 alleles were detected using the 16 microsatellite loci. The average number of alleles per locus was 7.52 (0.49), 7.35 (0.54), 6.3 (0.44), and 6 (0.38) for the Arab-Barb, Barb, Arabian, and English Thoroughbred breeds, respectively. The observed heterozygosities ranged from 0.63 (0.03) in the English Thoroughbred to 0.72 in the Arab-Barb breeds, whereas the expected heterozygosities were between 0.68 (0.02) in the English Thoroughbred and 0.73 in the Barb breeds. All FST values calculated by pairwise breed combinations were significantly different from zero (p  <  0.05) and an important genetic differentiation among breeds was revealed. Genetic distances, the factorial correspondence, and principal coordinate analyses showed that the important amount of genetic variation was within population. These results may facilitate conservation programs for the studied breeds and enhance preserve their genetic diversity.

scholarly journals Molecular evidence of species- and subspecies-level distinctions in the rare Orchis patens s.l. and implications for conservation

2021 ◽  
Vol 30 (5) ◽  
pp. 1293-1314
Author(s):  
Jacopo Calevo ◽  
Roberta Gargiulo ◽  
Leif Bersweden ◽  
Juan Viruel ◽  
Cristina González-Montelongo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Canary Islands ◽  
Population Decline ◽  
Small Population ◽  
Disjunct Distribution ◽  
Molecular Evidence ◽  
Genetic Diversity And Structure ◽  
Conservation Actions

AbstractCharacterizing genetic diversity and structure of populations is essential for the effective conservation of threatened species. Orchis patens sensu lato is a narrowly distributed tetraploid species with a disjunct distribution (i.e., Northern Italy, North Africa and the Canary Islands), which is facing a severe decline. In this study, we evaluated levels of genetic diversity and population structuring using 12 new nuclear microsatellite markers. Our analyses of genetic differentiation based on multiple approaches (Structure analysis, PCA analysis, and F-statistics using the ploidy-independent Rho-index) showed that gene flow is low across the range of O. patens s.l., particularly in the Canary Islands. Clear differences in allele frequencies between Italy, Algeria and the Canary Islands underlie the genetic differentiation retrieved. Our study provides support for the recognition of O. canariensis as a sister species to O. patens and the separation of the Italian populations as a new subspecies of O. patens. Despite the high heterozygosity values found in all populations (ranging from 0.4 to 0.7), compatible with the tetraploid status of the species, small population sizes and reduced gene flow will be likely detrimental for the different populations in the long term, and we recommend immediate conservation actions to counteract further fragmentation and population decline.

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