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

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.

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

Australian Journal of Botany ◽

10.1071/bt16128 ◽

2016 ◽

Vol 64 (8) ◽

pp. 687 ◽

Cited By ~ 5

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.

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Spatial genetic structure and asymmetrical gene flow within the Pacific walrus

Journal of Mammalogy ◽

10.1644/11-mamm-a-344.1 ◽

2012 ◽

Vol 93 (6) ◽

pp. 1512-1524 ◽

Cited By ~ 9

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.

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

Revista de Biología Tropical ◽

10.15517/rbt.v65i4.27882 ◽

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.

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

10.1101/2020.03.23.004622 ◽

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.

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

PLoS ONE ◽

10.1371/journal.pone.0248672 ◽

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.

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Genetic diversity of Dactylorhiza incarnata (Orchidaceae) in northern Poland

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.3496 ◽

2016 ◽

Vol 85 (2) ◽

Cited By ~ 3

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 Dactylorhiza incarnata var. incarnata 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, D. incarnata var. incarnata 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 (A = 4.67; Ae = 2.73; Rs = 4.48; Ho = 0.438; FIS = 0.224), which varied among the studied populations (A: 2.17–3.67; Ae: 1.55–2.69; Rs: 1.31–1.61; Ho: 0.292–0.631; FIS: −0.283–0.340). A considerable overabundance of homozygotes was detected in four populations (FIS 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 (ta = 0.980), and primarily indicated a tendency to out-cross within the species. Moderate genetic differentiation was found among the studied populations (FST = 0.149; RST = 0.174; p < 0.05). The differentiation of the populations corresponded to relatively low gene flow value (Nm = 0.426) among populations, which amounted to only one migrant every second generation.

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

Canadian Journal of Forest Research ◽

10.1139/x99-067 ◽

1999 ◽

Vol 29 (9) ◽

pp. 1311-1316 ◽

Cited By ~ 9

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.

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

Parasites & Vectors ◽

10.1186/s13071-019-3801-4 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 2

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.

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Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Heredity ◽

10.1038/s41437-021-00413-0 ◽

2021 ◽

Author(s):

Yael S. Rodger ◽

Alexandra Pavlova ◽

Steve Sinclair ◽

Melinda Pickup ◽

Paul Sunnucks

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Differentiation ◽

Evolutionary History ◽

Livestock Grazing ◽

Genetic Connectivity ◽

Evolutionary Divergence ◽

Common Component ◽

A Genome ◽

Eastern Australia

AbstractConservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

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Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

10.21203/rs.3.rs-779119/v1 ◽

2021 ◽

Author(s):

Guai-qiang Chai ◽

Yizhong Duan ◽

Peipei Jiao ◽

Zhongyu Du ◽

Furen Kang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Association Studies ◽

Natural Populations ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Future Design ◽

Ammopiptanthus Nanus ◽

Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

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