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 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.

Genetic diversity and gene flow patterns in two riverine plant species with contrasting life-history traits and distributions across a large inland floodplain

2020 ◽  
Vol 68 (5) ◽  
pp. 384
Author(s):  
William Higgisson ◽  
Dianne Gleeson ◽  
Linda Broadhurst ◽  
Fiona Dyer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Water Resource ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Resource Development ◽  
Water Resource Development ◽  
Floodplain River

Gene flow is a key evolutionary driver of spatial genetic structure, reflecting demographic processes and dispersal mechanisms. Understanding how genetic structure is maintained across a landscape can assist in setting conservation objectives. In Australia, floodplains naturally experience highly variable flooding regimes that structure the vegetation communities. Flooding plays an important role, connecting communities on floodplains and enabling dispersal via hydrochory. Water resource development has changed the lateral-connectivity of floodplain-river systems. One possible consequence of these changes is reduced physical and subsequent genetic connections. This study aimed to identify and compare the population structure and dispersal patterns of tangled lignum (Duma florulenta) and river cooba (Acacia stenophylla) across a large inland floodplain using a landscape genetics approach. Both species are widespread throughout flood prone areas of arid and semiarid Australia. Tangled lignum occurs on floodplains while river cooba occurs along rivers. Leaves were collected from 144 tangled lignum plants across 10 sites and 84 river cooba plants across 6 sites, on the floodplain of the lower and mid Lachlan River, and the Murrumbidgee River, NSW. DNA was extracted and genotyped using DArTseq platforms (double digest RADseq). Genetic diversity was compared with floodplain-river connection frequency, and genetic distance (FST) was compared with river distance, geographic distance and floodplain-river connection frequency between sites. Genetic similarity increased with increasing floodplain-river connection frequency in tangled lignum but not in river cooba. In tangled lignum, sites that experience more frequent flooding had greater genetic diversity and were more genetically homogenous. There was also an isolation by distance effect where increasing geographic distance correlated with increasing genetic differentiation in tangled lignum, but not in river cooba. The distribution of river cooba along rivers facilitates regular dispersal of seeds via hydrochory regardless of river level, while the dispersal of seeds of tangled lignum between patches is dependent on flooding events. The genetic impact of water resource development may be greater for species which occur on floodplains compared with species along river channels.

Genetic structure and proposed conservation strategy for natural populations of Calycanthus chinensis Cheng et S.Y. Chang (Calycanthaceae)

2008 ◽  
Vol 88 (1) ◽  
pp. 179-186 ◽  
Author(s):  
Chu-Chuan Fan ◽  
Nicola Pecchioni ◽  
Long-Qing Chen
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Gene Diversity ◽  
Genetic Relationships ◽  
Natural Populations ◽  
Population Level ◽  
Conservation Strategy ◽  
Information Index

Calycanthus chinensis Cheng et S.Y. Chang, a tertiary relic species in China, is a shade-loving and deciduous bush withan elegant shape and beautiful flower of high ornamental value. It was widely planted in gardens and miniature scapes in China.The objective of this study was to characterize the genetic variation and structure in the three extant populations of the species, in order to provide useful information for a future conservation strategy. Twenty-two of 120 RAPD primers were selected and a total of 257 stable and clear DNA fragments were scored. Calycanthus chinensis showed a lower level of genetic diversity. At the population level, the percentage of polymorphic loci, Nei's gene diversity and Shannon’s information index were 40.9%, 0.1641 and 0.2386, respectively; while at the species level, the corresponding values were 59.1%, 0.2097 and 0.3123, respectively. The estimates of genetic differentiation based on Shannon’s information index (0.2360), Nei’s gene diversity (0.2175) and AMOVA (24.94%) were very similar, and significantly higher than the average genetic differentiation reported in outcrossed spermatophyte. So it suggested high genetic differentiation emerged among populations of C. chinensis. Genetic relationships among populations were assessed by Nei’s standard genetic distance, which suggested that the Tiantai population was genetically distinct from the other two populations. Moreover, the genetic distance was significantly correlated with geographical distance among populations (r = 0.997, t > t0.05). The gene flow (Nm) was 0.8994, indicating that gene exchange among populations was restricted. A conservation strategy was proposed based on the low gene flow and habitat deterioration, which are contributing to the endangered status of this species. Key words: Genetic diversity, endangered plant, population genetics, RAPD

scholarly journals High-Level Gene Flow Restricts Genetic Differentiation in Dairy Cattle Populations in Thailand: Insights from Large-Scale Mt D-Loop Sequencing

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1680
Author(s):  
Nattakan Ariyaraphong ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
Thitipong Panthum ◽  
Syed Farhan Ahmad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Differentiation ◽  
Dairy Cattle ◽  
Large Scale ◽  
Genetic Relationships ◽  
Extensive Study ◽  
Distribution Analysis ◽  
Cattle Breeds ◽  
D Loop

Domestication and artificial selection lead to the development of genetically divergent cattle breeds or hybrids that exhibit specific patterns of genetic diversity and population structure. Recently developed mitochondrial markers have allowed investigation of cattle diversity worldwide; however, an extensive study on the population-level genetic diversity and demography of dairy cattle in Thailand is still needed. Mitochondrial D-loop sequences were obtained from 179 individuals (hybrids of Bos taurus and B. indicus) sampled from nine different provinces. Fifty-one haplotypes, of which most were classified in haplogroup “I”, were found across all nine populations. All sampled populations showed severely reduced degrees of genetic differentiation, and low nucleotide diversity was observed in populations from central Thailand. Populations that originated from adjacent geographical areas tended to show high gene flow, as revealed by patterns of weak network structuring. Mismatch distribution analysis was suggestive of a stable population, with the recent occurrence of a slight expansion event. The results provide insights into the origins and the genetic relationships among local Thai cattle breeds and will be useful for guiding management of cattle breeding in Thailand.

scholarly journals Small-scale spatial genetic structure of Asarum sieboldii metapopulation in a valley

2021 ◽  
Vol 45 (1) ◽  
Author(s):  
Hyeon Jin Jeong ◽  
Jae Geun Kim
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Spatial Genetic Structure ◽  
Dispersal Distance ◽  
Forest Understory ◽  
Small Scale ◽  
Low Density ◽  
Stochastic Events

Abstract Background Asarum sieboldii Miq., a species of forest understory vegetation, is an herbaceous perennial belonging to the family Aristolochiaceae. The metapopulation of A. sieboldii is distributed sparsely and has a short seed dispersal distance by ants as their seed distributor. It is known that many flowers of A. sieboldii depend on self-fertilization. Because these characteristics can affect negatively in genetic structure, investigating habitat structure and assessment of genetic structure is needed. A total of 27 individuals in a valley were sampled for measuring genetic diversity, genetic distance, and genetic differentiation by RAPD-PCR. Results The habitat areas of A. sieboldii metapopulation were relatively small (3.78~33.60 m2) and population density was very low (five to seven individuals in 20×20 m quadrat). The habitat of A. sieboldii was a very shady (relative light intensity = 0.9%) and mature forest with a high evenness value (J = 0.81~0.99) and a low dominance value (D = 0.19~0.28). The total genetic diversity of A. sieboldii was quite high (h = 0.338, I = 0.506). A total of 33 band loci were observed in five selected primers, and 31 band loci (94%) were polymorphic. However, genetic differentiation along the valley was highly progressed (Gst = 0.548, Nm = 0.412). The average genetic distance between subpopulations was 0.387. The results of AMOVA showed 52.77% of variance occurs among populations, which is evidence of population structuring. Conclusions It is expected that a small-scale founder effect had occurred, an individual spread far from the original subpopulation formed a new subpopulation. However, geographical distance between individuals would have been far and genetic flow occurred only within each subpopulation because of the low density of population. This made significant genetic distance between the original and new population by distance. Although genetic diversity of A. sieboldii metapopulation is not as low as concerned, the subpopulation of A. sieboldii can disappear by stochastic events due to small subpopulation size and low density of population. To prevent genetic isolation and to enhance the stable population size, conservative efforts such as increasing the size of each subpopulation or the connection between subpopulations are needed.

scholarly journals Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243999
Author(s):  
Ke-Xin Zhu ◽  
Shan Jiang ◽  
Lei Han ◽  
Ming-Ming Wang ◽  
Xing-Ya Wang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Management Strategies ◽  
Geographic Distance ◽  
Northern China ◽  
Economic Losses ◽  
Chilo Suppressalis

The rice stem borer (RSB), Chilo suppressalis (Lepidoptera: Pyralidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively control this pest, we investigated the genetic diversity, genetic differentiation and genetic structure of 16 overwintering populations in the typical bivoltine areas of northern China based on 12 nuclear microsatellite loci. Moderate levels of genetic diversity and genetic differentiation among the studied populations were detected. Neighbour-joining dendrograms, Bayesian clustering and principal coordinate analysis (PCoA) consistently divided these populations into three genetic clades: western, eastern and northern/central. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. Bottleneck analysis illustrated that RSB populations had not undergone severe bottleneck effects in these regions. Accordingly, our results provide new insights into the genetic relationships of overwintering RSB populations and thus contribute to developing effective management strategies for this pest.

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 of Rocky Mountain bighorn sheep (Ovis canadensis canadensis) at the northern limit of their native range

2020 ◽  
Vol 98 (5) ◽  
pp. 317-330
Author(s):  
Samuel Deakin ◽  
Jamieson C. Gorrell ◽  
Jeffery Kneteman ◽  
David S. Hik ◽  
Richard M. Jobin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Rocky Mountains ◽  
Spatial Genetic Structure ◽  
Rocky Mountain ◽  
Bighorn Sheep ◽  
Ovis Canadensis ◽  
Fine Scale ◽  
Northern Portion

The Canadian Rocky Mountains are one of the few places on Earth where the spatial genetic structure of wide-ranging species has been relatively unaffected by anthropogenic disturbance. We characterized the spatial genetic structure of Rocky Mountain bighorn sheep (Ovis canadensis canadensis Shaw, 1804) in the northern portion of their range. Using microsatellites from 1495 individuals and mitochondrial DNA sequences from 188 individuals, we examined both broad- and fine-scale spatial genetic structure, assessed sex-biased gene flow within the northern portion of the species range, and identified geographic patterns of genetic diversity. We found that broad-scale spatial genetic structure was consistent with barriers to movement created by major river valleys. The fine-scale spatial genetic structure was characterized by a strong isolation-by-distance pattern, and analysis of neighborhood size using spatial autocorrelation indicated gene flow frequently occurred over distances of up to 100 km. However, analysis of sex-specific spatial autocorrelation and analysis of mitochondrial haplotype distributions failed to detect any evidence of sex-biased gene flow. Finally, our analyses reveal decreasing genetic diversity with increasing latitude, consistent with patterns of post-glacial recolonization of the Rocky Mountains.

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